United Stetea
Environmental Protection
Office of Water
Regulations and Standards
Washington, DC 20460
<&ERA Technical Support Manual:
Waterbody Surveys and
Assessments for Conducting
Use Attainability Analyses
Volume II: Estuarine Systems

The Technical Support Manual: Water Body Surveys and Assessments for
Conducting Use Attainability Analyses in Estuarine Systems contains
guidance prepared by EPA to assist States in implementing the revised Water
Quality Standards Regulation (48 FR 51400, November 8, 1983). This
document addresses the unique characteristics of estuarine systems and
supplements the Technical Support Manual: Water Body Surveys and
Assessments for Conducting Use Attainability Analyses (EPA, November,
1983). The central purpose of these documents is to provide guidance to
assist States in answering three central questions:
(1)	What are the aquatic protection uses currently being achieved in the
water body?
(2)	What are the potential uses that can be attained based on the
physical, chemical and biological characteristics of the waterbody?
(3)	What are the causes of any impairment of the uses?
Consideration of the suitability of a water body for attaining a given use
is an integral part of the water quality standards review and revision
process. EPA will continue to provide guidance and technical assistance to
the States in order to improve the scientific and technical bases of water
quality standards decisions. States are encouraged to consult with EPA at
the beginning of any standards revision project to agree on appropriate
methods before the analyses are initiated, and to consult frequently as
they are conducted.
Any questions on this guidance may be directed to the water quality
standards coordinators located in each of the EPA Regional Offices or to:
Elliot Lomnitz
Criteria and Standards Division (WH-585)
401 M Street S.W.
Washington, D.C. 20460
Steven Schatzow, Director
Office of Water Regulations and


EPA's Office of Water Regulations and Standards has prepared guidance to
accompany changes to the Water Quality Standards Regulation (48 FR 51400).
Programmatic guidance has been compiled and published in the Water Quality
Standards Handbook (EPA, December 1983). This document discusses the water
quality review and revision process; general programmatic guidance on
mixing zones, flow, and economic considerations; use attainability
analyses; and site specific criteria.
One of the major pieces of guidance in the Handbook is "Water Body Surveys
and Assessments for Conducting Use Attainability Analyses," This guidance
lays out the general framework for designing and conducting a use
attainability analysis, whose objective is to answer the questions:
1.	What are the aquatic life uses currently being achieved in the
water body?
2.	What are the potential uses that can be attained, based on the
physical, chemical and biological characteristics of the water
3.	What are the causes of impairment of the uses?
Technical guidance on conducting water body surveys and assessments was
provided in the Technical Support Manual: Water Body Surveys and
Assessments for Conducting Use Attainability Analyses (EPA, November 1983)
in response to requests by several States for additional information. The
Technical Support Manual essentially provides methods and tools for
freshwater evaluations, but does not cover estuarine water bodies. The
chapters presented in this volume address those considerations which are
unique to the estuary. Those factors which are common to the freshwater
and the estuarine system -- chemical evaluations in particular, are not
discussed in this volume. Thus it is important that those who will be
involved in the water body survey should also consult the 1983 Technical
Support Manual. The methods and procedures offered in these guidance
documents are optional and the States may apply them selectively, or they
may use their own techniques or methods for conducting use attainability
The technical material presented in this volume deals with the major
physical, chemical and biological attributes of the estuary: tides and
currents, stratification, substrate characteristics; the importance of
salinity, dissolved oxygen and nutrient enrichment; species diversity,
plant and animal populations, and physiological adaptations which permit
freshwater or marine organisms to survive in the estuary.
Given that estuaries are very complex receiving waters which are highly
variable in description and- are not absolutes in definition, size, shape,
aquatic life or other attributes, those who will be performing use

attainability analyses on estuarine systems should consider this volume as
a frame of reference froni which to initiate study design and execution, but
not as an absolute guide.

The term estuary is generally used to denote the lower reaches of a river
where tide and river flows interact. The generally accepted definition for
an estuary was provided by Pritchard in 1952: "An estuary is a semi-
enclosed coastal body of water having a free connection with the open sea
and containing a measureable quantity of seawater." This description has
remained remarkably consistent with time and has undergone only minor
revisions (Emery and Stevenson, 1957; Cameron and Pritchard, 1963). To
this day, such qualitative definitions are the most typical basis for
determining what does and what does not constitute an estuary.
Estuaries are perhaps the most important social, economic, and ecologic
regions in the United States. For example, according to the Department of
Commerce (DeFalco, 1967), 43 of the 110 Standard Metropolitan Statistical
Areas are on estuaries. Furthermore, recent studies indicate that many
estuaries, including Delaware Bay and Chesapeake Bay, are on the decline.
Thus, the need has arisen to better understand their ecological functions
to define what constitutes a "healthy" system, to define actual and
potential uses, to determine whether designated uses are impaired, and to
determine how these uses can be preserved or maintained. This is the basis
for the Use Attainability Analysis.
As part of such a program, there is a need to define impact assessment pro-
cedures that are simple, in light of the wide variability among estuaries,
yet adequately represent the major features of each system studied.
Estuaries are three-dimensional waterbodies which exhibit variations in
physical and chemical processes in all three directions (longitudinal,
vertical, and lateral) and also over time. However, following a careful
consideration of the major physical and chemical processes and the time
scales involved in use assessment, one can often define a simplified
version of the prototype system for study.
In this chapter, a discussion is presented of important estuarine features
and of major physical processes. A description of chemical evaluations is
also presented, although the discussion herein is very limited since an
extensive presentation was included in the earlier U.S. EPA Technical
Support Manual (U.S. EPA November 1983). From this background, guidance
for use attainability evaluations is given which considers the various
assumptions that may be made to simplify the complexity of the analysis,
while retaining an adequate description of the system. Finally, a frame-
work for selecting appropriate desk-top and computer models for use
attainability evaluations is outlined.
Estuarine flows are the result of a complex interaction of:

o	tides,
o	wind shear,
o	freshwater inflow (momentum and buoyancy),
o	topographic frictional resistance,
o	Coriolis effect,
o	vertical mixing, and
o	horizontal mixing.
In performing a use attainability study, one must simplify the complex
prototype system by determining which of these effects or combination of
effects is most important at the time scale of the evaluation. To do this,
it is necessary to understand each of these processes and their impacts on
the evaluation. A complete description of all of the above is beyond the
scope of this report. Rather, illustrated are some of the features of each
process, particularly in terms of magnitude and time scale.
Tides are highly variable throughout the United States, both in amplitude
and phase. Figure II-1 (NOAA 1983) shows some typical tide curves along
the Atlantic, Gulf of Mexico, and Pacific Coasts. Tidal amplitude can vary
from 1 foot or less along the Gulf of Mexico (e.g., Pensacola, Florida) to
over 30 feet in parts of Alaska (e.g.. Anchorage) and the Maritime
Provinces of Canada (e.g., the Bay of Fundy). Tidal phasing is a
combination of many factors with differing periods. However, in the United
States, most tides are predominantly based on 12.5-hour (semidiurnal), 25-
hour (diurnal) and 4-day (semi-lunar) combinations. In some areas, such as
Boston (Figure II-l), the tide is predominantly semidiurnal with 2 high
tides and 2 low tides each day. In others, such as along the Gulf of
Mexico, the tides are more typically mixed.
Tidal power is directly related to amplitude. This potential energy source
can promote increased mixing through increased velocities and interactions
with topographic features.
In many exposed bays or estuaries, particularly those in which tidal
forcing is smaller, wind shear can have a tremendous impact on circulation
patterns at time scales of a few hours to several days. An example is
Tampa Bay on the West Coast of Florida, where tidal ranges are
approximately 3 feet, and the terrain is generally quite flat. Wind-can be
produced from localized thunderstorms of a few hours duration, or from
frontal movements with durations on the order of days. Unlike tides, wind
is unpredictable in a real time sense. The usual approach to studying wind
driven circulations is to develop a wind rose (Figure 11 -2) from local
meteorological data, and base the study of impacts on statistically
significant magnitudes and directions, or on winds that might produce the
most severe impact.

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Figure 11-2. Typical Wind Rose. (H.C. Perkins, 1974)
Freshwater Inflows
Freshwater inflows from a major riverine source can be highly variable from
day to day and season to season. At the shorter time scale, the river may
be responding to a localized thunderstorm, or the passage of a front. In
many areas, however, the frequency of these events tends to group into a
season (denoted the wet season) which is distinct from the remainder of the
year (the dry season). The average monthly streamflow distributions in
Figure 11-3 illustrate that in Virginia the wet season is typically from
December to May and comes mainly from portal systems. In Florida, however,
the trend is reversed, with the wet season coinciding with the summer
months when localized thunderstorms predominate.
It is important to consider the effect of freshwater flows on estuarine
circulation, because streamflow is the only major mechanism which produces
a net cross sectional flow over long averaging times. A common approach 1s
to represent the estuary as a system drive by net freshwater flows in the
downstream directory with other effects averaged out and lumped into a
dispersion-type parameter. When using this assumption to evaluate the
estuary system, one must weigh the consequences very carefully.
Freshwater is less dense, and tends to "float" over seawater. In some
cases, freshwater may produce a residual 2-layer flow pattern (such as in

the James Estuary (Virginia) or Potomac Rivers) or even a 3-layer flow
pattern (as in Baltimore Harbor). The danger is to treat such a distinctly
2-layer system as a cross-sectionally averaged, river driven system, and
then try to explain why pollutants are observed upstream of a discharge
point when no mechanism exists to produce this effect using a one-
dimensional approach.
The estuary's topographic boundaries (bed and sides) produce frictional
resistance to local currents. In some estuaries with highly variable
geometries, this can produce a number of net nontidal (or tidally-averaged)
effects such as residual eddies near headlands or tidal rectification.
Pollutants trapped in residual eddies, perhaps from a wastewater treatment
plant outfall, may have very large residence times that are not predictable
from cross-sectionally averaged flows before such pollutants are,flushed
from the system.
Coriolis Effect
In wide estuaries, the Coriolis effect can cause freshwater to adhere to
the right-hand bank (facing the open sea) so that the surface slopes upward
to the right of the flow. The interface has an opposite slope to maintain
geostrophic balance. For specific configurations and corresponding flow
regimes, the boundary between outflow and inflow may actually cut the
surface (Figure 11-4a). This is the case in the lower reaches of the St.
Lawrence estuary, for example, where the well-defined Gaspe current holds
against the southern shore and counter flow is observed along the northern
side. This effect is augmented by tidal circulation which forces ocean
waters entering the estuary with the flood tide to adhere to the left side
of the estuary (facing the open sea), and the ebb flow to the right side.
Thus, as is often apparent from the surface salinity pattern in an estuary,
the outflow is stronger on the right-hand side (Figure 11-4b). The exact
location and configuration of the saltwater/freshwater interface depends on
the relative magnitude of the forces at play. Quantitative estimates of
various mixing modes in estuaries are discussed below.
Vertical Mixing
All mixing processes are caused by local differences in velocities and by
the fact that liquids are viscous (i.e., possess internal friction). In
the vertical direction, the most common mixing occurs between riverine
fresh waters and the underlying saline ocean waters.
If there were no friction, freshwater would flow seaward as a shallow layer
on top of the seawater. The layer would become shallower and the velocity
would decrease as the estuary widened toward its mouth. Friction between
the two types of water requires a balancing pressure gradient down-estuary,
explaining the salt wedge formation which deepens toward the mouth of the
estuary, as seen in Figure II-5. Friction also causes mixing along the
interface. A particularly well-defined salt wedge is- observed in the
estuary of the Mississippi River.

0 1 607500-RaDidan River near CulDeoer, Va. Drainage area. 472 sq.mi.
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02030500-Slafe River near Arvonia, Va.
Drainage area, 226 sq.mi.
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0 3 4 8 8000-N.F. Holston River near Saltville, Va Drjimqe area, 222 sq.mi.
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Figure 11-3. Monthly Average Streamflows for location in
Virginia, (from U. S. Geological Survey 1982)

a. Cross-section A-A looking
b. Surface Salinity Distribu-
tion (ppt).
Figure 11-4. Net Inflow and Outflow in a Tidal Estuary., Northern
If significant mixing does not occur along the freshwater/saltwater inter-
face, the layers of differing density tend to remain distinct and the
system is said to be highly stratified in the vertical direction. If the
vertical mixing is relatively high, the mixing process can almost
completely break down the density difference, and the system is called
well-mixed or homogeneous.
In sections of the estuary where there is a significant difference between
surface and bottom salinity levels over some specified depth (e.g., differ-
ences of about 5 ppt or greater over about a 10 foot depth), the water
column is regarded as highly stratified. An important impact of vertical
stratification on use attainability is that the vertical density differ-
ences significantly reduce the exchange of dissolved oxygen and other
constituents between surface and bottom waters. Consequently, persistent
stratification can result in a depression of dissolved oxygen (DO) in the
high salinity bottom waters that are cut off from the low salinity surface
waters. This is because bottom waters depend upon vertical mixing with
surface waters, which can take advantage of reaeration at the air-water
interface, to replenish DO that is consumed as a result of organic
materials within the water column and bottom sediments. In sections of the
estuary exhibiting significant vertical stratification, vertical mixing of
DO contributed by reaeration 1s limited to the low salinity surface waters.

As a result, persistent stratified conditions can cause the DO concentra-
tion 1n bottom water to fall to levels that cause stress on or mortality to
the resident communities of benthic organisms.
Another potential Impact of vertical stratification 1s that anaerobic con-
ditions 1n bottom waters can result 1n Increased release of nutrients such
as phosphorus and ammonia-nitrogen from bottom sediments. During later
periods or In sections of the estuary exhibiting reduced levels of
stratification, these Increased bottom sediment contributions of nutrlerlts
can eventually be transported to the surface water layer. These Increased
Figure 11-5. Layered Flow in a Salt-wedge Estuary (Longitudinal Profile).

nutrient loadings on surface waters can result in higher phytoplankton con-
centrations that can exert diurnal DO stresses and reduced light penetra-
tion for rooted aquatic plants. In summary, the persistence and areal
extent of vertical stratification is an important determinant of use at-
tainability within an estuary.
Horizontal Mixing
Mixing also occurs in the horizontal plane, although it is often neglected
in favor of vertical processes. As with vertical mixing, horizontal mixing
1s caused by localized velocity variations and internal friction, or vis-
cosity. The velocity variations are usually produced by the interactions
of topographic and bed or side frictional effects, resulting in eddies of
varying sizes. Thus, horizontal constituent distributions tend to be broken
down by differential advection, which when viewed as an average advection
(laterally, or cross-sectionally) is called dispersion.
It is often useful to consider some broad classifications of estuaries,
particularly in terms of features and processes which enable us to analyze
them in terms of simplified approaches. The most commonly used groupings
are based on geomorphology, stratification, circulation patterns, and time
Geomorphological CIassification
Over the years, a systematic structure of geomorphological classification
has evolved. Dyer (1973) and Fischer et al. (1979) identify four groups:
o	Drowned river valleys (coastal plain estuaries),
o	Fjords
o	Bar-built estuaries, and
o	Other estuaries that do not fit the first three classifications.
Typical	examples of North American estuaries are presented in Table 11-1.
Coastal plain estuaries are generally shallow with gently sloping bottoms,
with depths increasing uniformly towards the mouth. Such estuaries have
usually been cut by erosion and are drowned river valleys, often displaying
a dendritic pattern fed by several streams. A well-known example is
Chesapeake Bay. Coastal plain estuaries are usually moderately stratified
(particularly in the old river valley section) and can be highly influenced
by wind over short time scales.
Bar built estuaries are bodies of water enclosed by the deposition of a
sand bar off the coast through which a channel provides exchange with the
open sea, usually servicing rivers with relatively small discharges. These

Dominant	Degree of
Type	Long-Term Process Stratification	Examples
Coastal	River Flow	Moderate	Chesapeake Bay, MD/VA
Plain	James River, VA
Potomac River, MD/VA
Delaware Estuary, DE/NJ
New York Bight, NY
Bar Built	Wind	Low or None Little Sarasota Bay, FL
Apalachicola Bay, FL
Galveston Bay, TX
Roanoke River, VA
Albemarle Sound, NC
Pamlico Sound, NC
Fjords	Tide	High	Alberni Inlet, B.C.
Silver Bay, AL
Other Estuaries Various	Various	San Francisco Bay, CA
Columbia River, WA/OR

are usually unstable estuaries, subject to gradual seasonal and cata-
strophic variations in configuration. Many estuaries in the Gulf Coast and
Lower Atlantic Regions fall into this category. They are generally a few
meters deep, vertically well mixed and highly influenced by wind.
Fjords are characterized by relatively deep water and steep sides, and are
generally long and narrow. They are usually formed by glaciation, and are
more typical in Scandinavia and Alaska than the contiguous United States.
There are examples along the Northwest Pacific Ocean, such as Alberni Inlet
in British Columbia. The freshwater streams that feed a fjord generally
pass through rocky terrain. Little sediment is carried to the estuary by
the streams, and thus the bottom is likely to be a clean rocky surface.
The deep water of a fjord is distinctly cooler and more saline than the
surface layer, and the fjord tends to be highly stratified.
The remaining estuaries not covered by the above classification are usually
produced by tectonic activity, faulting, landslides, or volcanic eruptions.
An example is San Francisco Bay which was formed by movement of the San
Andreas Fault System (Dyer, 1973).
Strati fication
A second classification of estuarie-s is by the degree of observed strati-
fication, and was developed originally by Pritchard (1955) and Cameron and
Pritchard (1963). They considered three groupings (Figure 11-6):
o The highly-stratified (salt wedge) type
o Partially mixed estuary
o Vertically homogeneous estuary
Such a classification is intended for the general case of the estuary
influenced by tides and freshwater inflows. Shorter term events, such as
strong winds, tend to break down highly stratified systems by inducing
greater vertical mixing. Examples of different types of stratification are
presented in Table 11-2.
In the stratified estuary (Figure 11 -6a), large freshwater inflows ride
over saltier ocean waters, with little mixing between layers. Averaged
over a tidal cycle, the system usually exhibits net seaward movement in the
freshwater layer, and net landward movement in the salt layer, as salt
water is entrained into the upper layer. The Mississippi River Delta is an
example of this type of estuary.
As the interfacial forces become great enough to partially break down the
density differences, the system becomes partially stratified, or partially
well-mixed (Figure 11-6b). Tidal flows are now usually much greater than
river flows, and flow reversals in the lower layer may still be observed,
although they are generally not as large as for the highly stratified
system. Chesapeake Bay and the James River estuary are examples of this

(a) Stratified
0  1 ^ 0
(b) Partially mixed

(c) Well-mixed
Figure 11-6. Classification of Estuarine Stratification.

Highly Stratified
River Discharge
Mississippi River, LA
Mobile River, AL
Partially Mixed
Chesapeake Bay, MD/VA
James Estuary, VA
Potomac River, MD/VA
Vertically Homogeneous
Delaware Bay, DE/NJ
Raritan River, NJ
Biscayne Bay, FL
Tampa Bay.FL.
San Francisco Bay, CA
San Diego Bay, CA

In a well mixed system (Figure 11-6c), the river inflow is usually very
small, and the tidal flow is sufficient to completely break down the
stratification and thoroughly mix the system vertically. Such systems are
generally shallow so that the tidal amplitude to depth ratio is large and
mixing can easily penetrate throughout the water column. The Delaware and
Raritan River estuaries are examples of well-mixed systems.
Circulation Patterns
Circulation in an estuary (i.e., the velocity patterns as they change over
time) is primarily affected by the freshwater outflow, the tidal inflow,
and the effect of wind. In turn, the difference in density between outflow
and inflow sets up secondary currents that ultimately affect the salinity
distribution across the estuary. The salinity distribution is important in
that it affects the distribution of fauna and flora within the estuary. It
is also important because it is indicative of the mixing properties of the
estuary as they may affect the dispersion of pollutants, flushing proper-
ties, and additional factors such as friction forces and the size and
geometry of the estuary contribute to the circulation patterns."
The complex geometry of estuaries, in combination with the presence of
wind, the effect of the earth's rotation (Coriolis effect), and other
effects, often results in residual currents (i.e., of longer period than
the tidal cycle) that strongly influence the mixing processes in estuaries.
For example, uniform wind over the surface of an estuary produces a net
wind drag force which may cause the center of mass of the water in the
estuary to be displaced toward the deeper side since there is more water
there. Hence a torque is induced causing the water mass to rotate.
In the absence of wind, the pure interaction of tides-and estuary geometry
may also cause residual currents. For example, flood flows through narrow
inlets set up so-called tidal jets, which are long and narrow as compared
to the ebb flows which draw from a larger area of the estuary, thus forcing
a residual circulation from the central part of the estuary to the sides
(Stommel and Farmer, 1952). The energy available in the tide is in part
extracted to drive regular circulation patterns whose net result is similar
to what would happen if pumps and pipes were installed to move water about
in circuits. This is why this type of circulation is referred to as "tidal
pumping" to differentiate from wind and other circulation (Fisher, et al.,
Tidal "trapping" is a mechanism -- present in long estuaries with side
embayments and small branching channels -- that strongly enhances
longitudinal dispersion. It is explained as follows. The propagation of
the tide in an estuary -- which represents a balance between the water mass
inertia, the hydraulic pressure force due to the slope of the water
surface, and the retarding bottom friction force  results in main channel
tidal elevations and velocities that are not in phase. For example, high
water occurs before high slack tide and low water before low slack tide
because the momentum of flow in the main channel causes the current to
continue to flow against an opposing pressure gradient. In contrast, side
channels which have less momentum can reverse the current direction faster,

thus "trapping" portions of the main channel water which are then available
for further longitudinal dispersion during the next flood tide.
Time Scales
The consideration of the time scales of the physical processes being
evaluated is very important for any water quality study. Short-term
conditions are much more influenced by a variety of short-term events which
perhaps have to be analyzed to evaluate a "worst case" scenario. Longer
term (seasonal) conditions are influenced predominantly by events which are
averaged over the duration of that time scale.
The key to any study is to identify the time scale of the impact being
evaluated and then analyze the forcing functions over the same time scale.
As an example, circulation and mass transport in the upper part of
Chesapeake Bay can be wind driven over a period of days, but is river
driven over a period of one month or more. Table 11 -3 lists the major
types of forcing functions on most estuarine systems and gives some idea of
their time scales.
"Segmentation" of an estuary can provide a useful framework for evaluating
the influence of estuarine physical characteristics such as circulation,
mixing, salinity, and geomorphology on use attainability. Segmentation is
the compartmentalizing of an estuary into subunits with homogeneous
physical characteristics. In the absence of water pollution, physical
characteristics of different regions of the estuary tend to govern the
suitability for major water uses. Therefore, one major objective of
segmentation is to subdivide the estuary into segments with relatively
homogeneous physical characteristics so that differences in the biological
communities among similar segments may be related to man-made alterations.
Once the segment network is established, each segment can be subjected to a
use attainability analysis. In addition, the segmentation process offers a
useful management structure for monitoring conformance with water quality
goals in future years.
The segmentation process is an evaluation tool which recognizes that an
estuary is an interrelated ecosystem composed of chemically, physically,
aind biologically diverse areas. It assumes that an ecosystem as diverse as
an estuary cannot be effectively managed as only one unit, since different
uses and associated water quality goals will be appropriate and feasible
for different regions of the estuary. The segmentation approach to use
attainability assessment and water quality management has been successfully
applied to several major receiving water systems, most notably Chesapeake
Bay, the Great Lakes, and San Francisco Bay.
A potential source of concern about the construction and utility of the
segmentation scheme for use attainability evaluations is that the estuary
is a fluid system with only a few obvious boundaries, such as the sea
surface and the sediment-water interface. Boundaries fixed in space are to
be imposed on an estuarine system where all components are in communication
with each other following a pattern that is highly variable in time. Fixed
boundaries may seem unnatural to scientists, managers, and users, who are

Forcing Function	Time Scale
One cycle	0.5-1 day
Neap/Spring	14 days
Thunderstorm	1-4 hours
Frontal Passage	1-3 days
Thunderstorm	0.5-1 day
Frontal Passage	3-7 days
Wet/Dry Seasons	4-6 months

more likely to view the estuary as a continuum than as a system composed of
separable parts. The best approach to dealing with such concerns is a
segmentation scheme that stresses the dynamic nature of the estuary. The
scheme should emphasize that the segment boundaries are operationally
defined constructs to assist in understanding a changeable, intercommuni-
cating system of channels, embayments, and tributaries.
In order to account for the dynamic nature of the estuary, it is recommend-
ed that estuarine circulation patterns be a prominent factor in delineating
the segment network. Circulation patterns control the transport of and
residence times for heat, salinity, phytoplankton, nutrients, sediment, and
other pollutants throughout the estuary. Salinity should be another impor-
tant factor in delineating the segment network. The variations in salinity
concentrations from head of tide to the mouth typically produce a separa-
tion of biological communities based on salinity tolerances or preferences.
A segmentation scheme based upon physical processes such as circulation and
salinity should track very well with the major chemical and biological
processes. However, after developing a network based upon physical
characteristics, segment boundaries can be refined with available chemical
and biological data to maximize the homogeneity of each segment.
To illustrate the segmentation approach to evaluating relationships between
physical characteristics and use attainability, the segmentation scheme
applied to Chesapeake Bay is described below. While most of the estuaries
subjected to use attainability evaluations will be considerably smaller and
less diverse than Chesapeake Bay, the principles illustrated in the
following example can serve as useful guidance for most estuary evaluations
regardless of the spatial scale. Figure 11-7 shows the main stem and
tributary segments defined for Chesapeake Bay by the U.S. Environmental
Protection Agency's Chesapeake Bay Program (U.S. EPA Chesapeake Bay
Program 1982). As may be seen, the segment network consists of eight main
stem segments designated by the prefix "CB" and approximately forty
segments covering major embayments and tributaries. The methodology for
delineating the main stem segments will be described first, followed by a
discussion of the major embayments and tributaries.
Starting at the uppermost segment and working down the main stem, the
boundary between CB-1 and CB-2 separates the mouth of the Susquehanna River
from the upper Bay and lies in the region of maximum penetration of salt-
water at the head of the Bay. South of this region most freshwater
plankton would not be expected to grow and flourish, although some may be
continually brought into the area by the Susquehanna River.
The boundary between CB-2 and CB-3 is the southern limit of the turbidity
maximum, a region where suspended sediment causes light limitation of
phytoplankton production most of the year. This boundary also coincides
with the long-term summer average for the 5 parts per thousand (ppt)
salinity contour which is an important physiological parameter for oysters.
The boundary between CB-3 and CB-4 is located at the Chesapeake Bay Bridge.
It marks the northern limit of the 10 ppt salinity contour and of deep
water anaerobic conditions in Chesapeake Bay stratification. In segment

Figure II-7. Chesapeake Bay Program segments used in data
analysis.(from U.S.EPA Chesapeake Bay Program 1982)

CB-4, water deeper than about 30 ft usually experiences oxygen depletion in
summer which may result in oxygenless conditions and hydrogen sulfide
production. When anaerobic conditions occur, these deep waters are toxic
to fish, crabs, shellfish, and other benthic animals. Due to the increased
release of nutrients from bottom sediments under oxygenless conditions, the
anaerobic layer is also rich in phosphorus and ammonia-N which may reach
surface waters by diffusion, mixing, and vertical advection either later in
the year or in less stratified sections of the Bay. In spring, the region
near the bridge is the site where phytoplankton and fish larvae that travel
in .the deep layer from the Bay mouth are brought to the surface by a
combination of physical processes.
The boundary between CB-4 and CB-5 was established at a narrows. Below
this point, the Patuxent and Potomac Rivers intersect the main stem of the
Bay. It is characterized by average summer salinities of 12 to 13 ppt and
is located at the approximate midpoint of the area subject to bottom water
anaerobic conditions during the summer.
The boundary between CB-5 and CB-6/7 approximates the 18 ppt salinity
contour and the southern limit of significant vertical stratification and
anaerobic conditions in the bottom waters. Most of the deeper areas of the
Bay are found in segment CB-5. As mentioned earlier, the bottom waters of
segments CB-4 and CB-5 experience considerable nutrient enrichment during
the summer when phosphorus and ammonia-N are released from bottom
sediments. This region also exhibits high nitrate-N concentrations in the
fall when the ammonia-N accumulated in summer is oxidized. The southern
boundary of CB-5 also approximates the region where the elevated nitrate-N
concentrations from the relatively high streamflows during the spring
season becomes a critical factor in phytoplankton growth.
The boundary between CB-6 and CB-7 horizontally divides the lower Bay into
two regions with different circulation patterns. North of this boundary,
the Bay's density stratification results in two distinct vertical layers,
with bottom waters moving in a net upstream flow and the surface layer
flows moving downstream. Between this boundary and the Bay mouth the
density distribution tends toward a cross-stream (i.e., horizontal)
gradient rather than a vertical gradient. Net advective flows throughout a
vertically well-mixed water column tend to flow northward in segment CB-7
and southward in CB-6 and CB-8. This pronounced horizontal gradient also
exists across the Bay mouth. Thus, plankton and fish larvae are brought
into the Bay with the higher salinity ocean waters along the eastern side
of the lower Bay until they become entrained into the lower layer at
segment CB-5 and are transported up the Bay to grow and mature.
Eastern shore embayments such as .Eastern Bay (EE-1), the subestuary of the
Choptank River (EE-2) and the Pocomoke and Tangier Sounds (EE-3) have
salinities similar to adjacent Bay waters, and they are shallow enough to
permit light penetration necessary for the growth of submerged aquatic
vegetation (SAVs). These areas provide shelter for many benthic inver-
tebrates and small fish which make an important contribution to the Bay's
rich environment.

Boundaries have been delineated at the mouths of the Bay's major tributar-
ies. These boundaries define the sources of freshwater, sediment, nutri-
ents, and other constituents delivered to the main stem of the Bay. Along
these boundaries, frontal zones between the tributary and main stem waters
tend to concentrate detrital matter and nutrients, with circulation
patterns governing the transport of many organisms to this food source.
The major tributaries are further subdivided into three segment classifica-
tions: tidal fresh (TF), river estuarine transition zone (RET), and lower
subestuary (LE). The tidal fresh segments are biologically important as
spawning areas for anadromous and semianadromous fish such as the alewife,
herrings, shad, striped bass, white perch and yellow perch. There are also
freshwater species which are resident in these areas such as catfish,
minnows and carps. Algal blooms tend to be most prolific within the tidal
fresh zone. The extent of these blooms is dependent upon nutrient supply, a
range of factors such as retention time, and light availability. Most of
the algal species that can flourish within tidal fresh segments are
Inhibited as they encounter the more saline waters associated, with the
transition zone.
The highest concentration of suspended solids is found at the interface of
fresh and saline waters and it approximates the terminus of density
dependent estuarine circulation. The area where this phenomenon occurs is
typically referred to as the "turbidity maximum" zone. The significance of
this area lies in Its Value as a sediment trap entraining not only material
introduced upstream but, additionally, material transported in bottom
waters from downstream. This mechanism also tends to concentrate any
material associated with the entrained sediment. For example, Kepone
accumulations within the James River_estuary are highest in the turbidity
maximum zone.
The final segment type found within the major tributaries is identified as
the lower subestuary segment. This area extends from the turbidity maximum
to the point where the tributary intersects the main stem of the Bay.
Highly productive oyster bars are found in these segments. There 1s a
heavy concentration of oyster bars in the lower subestuaries because of the
favorable depth, salinities, and substrate. In general, the oyster bars
are located in depths of less than 35 feet in salinities greater than 7-8
ppt and on substrates which are firm. Seasonal depressions of dissolved
oxygen 1n bottom waters prevent the establishment of oyster bars in most
waters over 35 feet deep.
This section provides a brief discussion of chemical indicators of aquatic
use attainment for estuaries. Three clarifications are necessary before
beginning this discussion. First, while it is useful to refer to these
parameters as "chemical" characteristics to distinguish them from the
physical and biological parameters in a use attainability evaluation, these
character!"sties are traditionally referred to as water quality criteria and
are referred to as such in other sections of this report. Second,
chlorophyll-a is introduced in this section rather than in Chapter III
because it is the primary impact indicator for chemicals such as nitrogen

and phosphorus. Third, because an extensive discussion of chemical water
quality indicators is presented in the earlier U.S. EPA Technical Support
Manual (U.S. EPA November 1983), the discussion herein is very limited.
Manual users who are interested in a more extensive discussion are referred
to the previous volume.
The most critical water quality indicators for aquatic use attainment in an
estuary are dissolved oxygen, nutrients and chlorophyll-a, and toxicants.
Dissolved oxygen (DO) is an important water quality indicator for all
fisheries uses. The DO concentration in bottom waters is the most critical
indicator of survival and/or density and diversity for most shellfish and
an important indicator for finfish. DO concentrations at mid-depth and
surface locations are also important indicators for finfish. In evaluating
use attainability, assessments of DO impacts should consider the relative
contributions of three different sources of oxygen demand: (a)
photosynthesis/respiration demand from phytoplankton; (b) water column
demand; and (c) benthic oxygen demand. If use impairment is occurring,
assessments of the significance of each oxygen sink can be used to evaluate
the feasibility of achieving sufficient pollution control to attain the
designated use.
Chlorophyll-a is the most popular indicator of algal concentrations and
nutrient overenrichment which in turn can be related to diurnal DO
depressions due to algal respiration. Typically, the control of phosphorus
levels can limit algal growth in the upper end of the estuary, while the
control of nitrogen levels can limit algal growth near the mouth of the
estuary; however, these relationships are dependent upon factors such as
N:P ratios and light penetration potential which can vary from one estuary
to the next, thereby producing different limiting conditions within a given
estuary. Excessive phytoplankton concentrations, as indicated by
chl orophyll-a levels, can cause adverse DO impacts such as: (a) wide
diurnal variations in surface DO's due to daytime photosynthetic oxygen
production and nighttime oxygen depletion by respiration, and (b) depletion
of bottom DO's through the decomposition of dead algae. Thus, excessive
chlorophyl1-a levels can deplete the oxygen resources required for bottom
water fisheries, exert stress on the oxygen resources of surface water
fisheries, and upset the balance of the detrital foodweb in the seagrass
community through the production of excessive organic matter.
Excessive chlorophyl1-a levels also result in shading which reduces light
penetration for submerged aquatic vegetation. Consequently, the prevention
of nutrient overenrichment is probably the most important water quality
requirement for a healthy SAV community.
Blooms of certain phytoplankton can also be toxic to fish. For example,
blooms of the toxic "red tide" organism during the early 1970's resulted in
extensive fish kills in several Florida estuaries.
The nutrients of concern in the estuary are nitrogen and phosphorus. Their
sources typically are discharges from sewage treatment plants and Indus-
tries, and runoff from urban and agricultural areas. Increased nutrient,
levels lead to phytoplankton blooms and a subsequent reduction in DO
levels, as discussed above. In addition, algal blooms decrease the depth

to which light is able to penetrate, thereby affecting SAV populations in
the estuary.
Sewage treatment plants are typically the major source of nutrients to
estuaries in urbanized areas. Agricultural land uses and urban land uses
represent significant nonpoint sources of nutrients. Often wastewater
treatment plants are the major source of phosphorus loadings while nonpoint
sources tend to be major contributors of nitrogen. In estuaries located
near highly urbanized areas, municipal discharges probably will dominate
the point source nutrient contributions. Thus, it is important to base
control strategies on an understanding of the sources of each type of
nutrient, both in the estuary and in its feeder streams.
In the Chesapeake Bay, an assessment of total nitrogen, total phosphorus,
and N:P ratios indicates that regions where resource quality is currently
moderate to good have lower concentrations of ambient nutrients, and N:P
ratios between 10:1 and 20:1, indicating phosphorus-limited algal growth.
Regions characterized by little or no SAV's (i.e., phytoplankton-dominated
systems) or massive algal blooms had high nutrient concentrations and
significant variations in the N:P ratios. Moving a system from one class
to another could involve either a reduction of the limiting nutrient (N or
P) or a reduction of the non-limiting nutrient to a level such that it
becomes limiting. For example, removal of P from a system characterized by
massive algal blooms could force it to become a more desirable
phytoplankton-dominated system with a higher N:P ratio.
Clearly the levels of both nitrogen and phosphorus are important deter-
minants of the uses that can be attained in an estuary. Because point
sources of nutrients are typically much more amenable to control than
nonpoint sources, and because nutrient (phosphorus) removal for municipal
wastewater discharges is typically less expensive than nitrogen removal
operations, the control of phosphorus discharges is often the method of
choice for the prevention or reversal of use impairment in the upper
estuary (i.e., tidal fresh zone). However, the nutrient control programs
for the upper estuary can have an adverse effect on phytopiankton growth 1n
the lower estuary (i.e., near the mouth) where nitrogen is typically the
critical nutrient for eutrophlcation control. This is because the
reduction of phytoplankton concentrations in the upper estuary will reduce
the uptake and settling of the non-limiting nutrient which is typically
nitrogen, thereby resulting in increased transport of nitrogen through the
upper estuary to the lower estuary where it is the limiting nutrient for
algal growth. The result is that reductions in algal blooms within the
upper estuary due to the control of one nutrient (phosphorus) can result in
increased phytoplankton concentrations in the lower estuary due to higher
levels of the uncontrolled nutrient (nitrogen). Thus, tradeoffs between
nutrient controls for the upper and lower estuary should be considered in
evaluating measures for preventing or reversing use impairment. The
Potomac Estuary is a good example of a system where tradeoffs between
nutrient controls for the upper and lower estuary are being evaluated.
The impacts of toxicants such as pesticides, herbicides, heavy metals and
chlorinated effluents are beyond the scope of this volume. However, the
presence of certain toxicants in excessive concentrations within bottom
sediments or the water column may prevent the attainment of water uses

(particularly fisheries propagation/harvesting and seagrass habitat uses)
in estuary segments which satisfy water quality criteria for DO,
chlorophyl1-a/nutrient enrichment, and fecal coliforms. Therefore, poten-
tial interferences from toxic substances need also to be considered in a
use attainability study.
Introducti on
Use attainability evaluations generally follow the conceptual outline:
o Determine the present use of the estuary,
o Determine whether the present use corresponds to the designated
o If the present use does not correspond to the designated use,
determine why, and
o Determine the optimal use for the system.
In assessing use levels for aquatic life protection, the first two items
are evaluated in terms of biological measurements and indices. However, if
the present use does not correspond to the designated use, one turns to
physical and chemical factors to explain the lack of attainment, and the
highest level the system can achieve.
The physical and chemical evaluations may proceed on several levels depend-
ing on the level of detail required, amount of knowledge available about
the system (and similar systems), and budget for the use- attainability
study. As a first step, the estuary is classified in terms of physical
processes (e.g., stratification, flushing time) so that it can be compared
with reference estuaries that exhibit similar physical characteristics.
Once a similar estuary is identified, it can be compared with the estuary
of interest in terms of water quality differences and differences in
biological communities which can be related to man-made alteration (i.e.,
pollution discharges). It is important to consider a number of simplifying
assumptions that can be made to reduce the conceptual complexity of the
prototype system for easier classification and more detailed analyses.
The second step is to perform desk-top or simple computer model calcula-
tions to improve the understanding of spatial and temporal water quality
conditions in the present system. These calculations include continuous
point source and simple box model type calculations, among others.
The third step is to perform more detailed analyses to investigate system
impact from known anthropogenic sources through the use of more sophisti-
cated computer models. These tools can be used to evaluate the system
response to removing individual point and nonpoint source discharges, so as
to assist with assessments of the cause(s) of any use impairment.

Desktop Evaluations of System Characteristics
This section discusses desktop analyses for evaluating relationships
between physical/chemical characteristics and use attainability. Desktop
evaluations that can provide guidance for the selection of appropriate
mathematical models for use attainability studies are also discussed.
Such evaluations can be used to characterize the complexity of an estuary,
important physical characteristics such as the level of vertical stratifi-
cation and flushing times, and violations of water quality criteria.
Depending upon the complexity of the estuary, these evaluations can
quantify the temporal and spatial dimensions of important physical/
chemical characteristics and relationships to use attainability needs as
summarized below:
1.	Vertical Stratification
a.	Temporal Scale: During which seasons does it occur? What is
the approximate duration of stratification in each season?
b.	Spatial Scale: How much area is subject to significant
stratification in each season?
2.	Flushing Times
a.	Temporal Scale: What are the flushing times for each major
estuary segment and the estuary as a whole?
b.	Spatial Scale: Which segments exhibit relatively high flushing
times? Relatively low flushing times?
3.	Violations of Water Quality Criteria (based upon statistical
analysis of measured data)
a.	Temporal Scale: Which seasons exhibit violations? How fre-
quently and for what durations do violations occur in each
season? Are the violations caused by short-term or long-term
phenomena? Short-term phenomena include: DO sags due to
combined sewer overflows or short-term nonpoint source
loadings, and diurnal DO variations due to significant
chlorophyl1-a levels. Long-term phenomena include: seasonal
eutrophication impacts due to nutrient loadings, seasonal DO
sag due to point source discharges, and seasonal occurrence of
anaerobic conditions in bottom waters due to persistent
vertical stratification.
b.	Spatial Scale: What is the spatial extent of the violations
(considering longitudinal, horizontal, and vertical direc-
4.	Relationship of Physical/Chemical Characteristics to Use Attain-
ability Needs

a.	Temporal Scale: Are use designations more stringent during
certain seasons (e.g., spawning season)? Are acceptable
physical/chemical characteristies required 100 percent of the
time in each season in order to ensure use attainability?
b.	Spatial Scale: Are there segments in the estuary which cannot
support designated uses due to physical limitations? Are
acceptable physical/chemical characteristics required in 100
percent of the estuary segment or estuary in order to ensure
attainability of the use?
Simp!ifying Assumptions. Zison et al. (1977) and Mills et al. (1982) list
a number of simplifying assumptions that can be made to reduce the com-
plexity of estuary evaluations. However, care must be taken to ensure that
such assumptions are applicable to the estuary under study and that they do
not reduce the problem to one which is physically or chemically unreason-
able. The following assumptions may be considered (Zison et al., 1977;
Mills et al., 1982):
a.	The present salinity distribution can be used as a direct measure
of the distribution of all conservative continuous flow pollutants
entering the estuary, and can be used as the basis for calculating
dispersion coefficients for a defined freshwater discharge con-
b.	The vertical water column 1s assumed to be well mixed from top to
c.	Flow and transport through the estuary is essentially one-
d.	The Coriolis effect may be neglected, which means that the estuary
is assumed to be laterally homogeneous,
e.	Only steady-state conditions will be considered, by using cal-
culations averaged over one or more tidal cycles to estimate a
freshwater driven flow within the estuary,
f.	Regular geometry may be assumed, at least over the length of each
segment, which means that topographically induced circulations are
g.	Only one river inflow can be used In the evaluation,
h.	No variations in tidal amplitude are permitted, and
1.- All water leaving the estuary on each tidal cycle is replaced by a
given percentage of "fresh" seawater.
The above list of assumptions are directed towards the specific objective
of reducing the estuary to a one-dimensional, quasi-steady-state system
amenable to desktop calculations. In reality these assumptions need to be
carefully weighed so that important processes are not omitted from the

One approach is to start with a completely three-dimensional system, deter-
mine which assumptions can reasonably be made, and see what the answer
means in terms of a simplified analysis. Procedures for making such
determinations are discussed in the next section, but several examples are
presented here for illustration.
The fact is that many narrow estuarine systems in which lateral homogeneity
can be assumed, also exhibit 2 or more layers of residual flow, making the
assumption of a one-dimensional system invalid. Conversely, given a
vertically well-mixed system like Biscayne Bay, one cannot assume lateral
homogeneity because the system is usually very wide wind mixing is too
significant to permit such a simple analysis.
Degree of Stratification.
Freshwater is lighter than saltwater. Therefore, the river may be thought
of as a source of buoyancy, of amount:
Buoyancy = ApgQf	(1)
where	Ap =	the,difference in density between sea and river water,
M/LJ	2
g =	acceleration of gravity.^L/T
Q, =	freshwater river flow, L /T
M =	units of mass
L =	units of length
T =	units of time
The tide on the other hand is a source of kinetic energy, equal to:
kinetic energy = pWUt	(2)
where	p = the seawater density,
W = the estuary width
IL = the square root of the averaged squared velocities.
The ratio of the above two quantities, called the "Estuarine Richardson
Number" (Fischer 1972), is an estuary characterization parameter which is
indicative of the vertical mixing potential of the estuary:
9 Qf
R = 	1	(3)

If R is very large (above 0.8), the estuary is typically considered to be
strongly stratified and' the flow to be typically dominated by density
currents. If R is very small, the estuary is typically considered to be
well-mixed and the density effects to be negligible.
Another desktop approach to characterizing the degree of stratification in
the estuary is to use a stratification-circulation diagram (Hansen and
Rattray 1966). The diagram (shown in Figure 11-8) requires the calculation
of two parameters:
Stratification Parameter = ^	(4)
and Circulation Parameter
where	AS = time averaged difference between salinity levels at
the surface and bottom of the estuary,
S = cross-sectional mean salinity,
U = net non-tidal surface velocity, and
= mean freshwater velocity through the section.
To apply the stratification-circulation diagram in Figure II-8, which is
based on measurements from a number of estuaries with known degrees of
stratification, calculate the parameters of Equation (4) and plot the
resulting point on the diagram. Type la represents slight stratification
as in a laterally homogeneous, well-mixed estuary. In Type lb, there is
strong stratification. Type 2 is partially well-mixed and shows flow
reversals with depth. In Type 3a the transfer is primarily advective, and
in Type 3b the lower layer is so deep, as in a fjord, that circulation does
not extend to the bottom. Finally, Type 4 represents the salt-wedge type
with intense stratification (Dyer 1973).
The purpose of the analysis is to examine the degree of vertical resolution
needed for the analysis. If the estuary is well-mixed, the vertical dimen-
sion may be neglected, and all constituents in the water column assumed to
be dispersed evenly throughout. If the estuary is highly stratified, at
least a 2-layer analysis must follow. For the case of a partially-mixed
system, a judgment call must be made. The James River may be considered as
an example which is partially stratified but was treated as a 2-layer
system for a recent toxics study (O'Connor, et al., 1983).
A final desktop method for characterizing the degree of stratification
is the calculation of the estuary number proposed by Thatcher and Harleman

b 1 ' r i	:


f'^'Y 3b \s,

in 10
I \ '^1
\ NM* \\ \
1o|  \
| 2o \ 3o
- 1 \


15 10 102 103 104 105


(Station code: M, Mississippi River mouth; C, Columbia
River estuary; J, James River estuary; NM, Narrows of
the Mersey estuary; JF, Strait of Juan.de Fuca; S,
Silver Bay. Subscripts h and 1 refer to high and low
river discharge; numbers indicate distance (in miles)
from mouth of the James River estuary.
Fioure 11-8. Stratification Circulation Diagram and Examples.

E . =	estuary number,
Pt =	tidal prism volume (volume between low and high tides),
Q- =	freshwater inflow,
T =	tidal period, and
F. =	densimetric Froude number =
layer velocity,
acceleration due to gravity,
density difference across interface,
density in layer, and
layer thickness.
Again, by comparing the calculated value with the values from known,
systems, one can infer the. degree of stratification present. The reader
should consult Thatcher and Harleman (1972) for further details.
Horizontal variations in density may still exist in a vertically well-mixed
estuary, resulting in circulation that is density driven in the horizontal
direction. It is helpful to understand density-driven circulation in an
estuary (baroclinic circulation) in order to assess its effect in relation
to turbulent diffusion on the landward transport of salinity. While
numerous studies have been performed over the years (e.g., Hansen and
Rattray 1965, 1966; Rigter, 1973), no unifying theory has emerged clearly
delineating longitudinal, transverse and vertical dispersion mechanisms.
This means that we still have to rely to a large extent on actual in-situ
Decisions about whether it is reasonable to neglect processes such as
Coriolis effects and wind is often judgmental. However, Cheng (1977) did
offer the following criterion for neglecting the Coriolis effect. The
criterion is based on the Rossby number:
Q, u

where	R = Rossby number,
u = characteristic wind velocity =1/2 peak surface
ft = earth's rotation rate, and
L = length of estuary,
Cheng suggested that for R <0.1, the Coriolis effect is small. Wind is
so highly variable and unpredictable that it is almost always neglected.
In general, 1t has little effect on steady-state conditions, except in
large open estuaries.
Finally, the use of simplified geometries, such as uniform depth and width
is highly judgmental. One may choose to neglect side embayments, minor
tributaries, narrows and inlets as a symplifying approach to achieve
uniform geometry. However, it is always important to consider the
consequences of this assumption.
Flushing Time. The time that is required to remove pollutant mass from a
particular point in an estuary (usually some upstream location) is called
the flushing time. Long flushing times are often indicative of poor water
quality conditions due to long residence times for pollutants. Flushing
time, particularly in a segmented estuary, can also be used in an initial
screening of alternate locations for facilities which discharge constitu-
ents detrimental to estuarine health if they persist in the water column
for lengthy periods.
Factors Influencing flushing times are tidal ranges, freshwater inflows,
and wind. All of these forcing functions vary over time, and may be
somewhat unpredictable (e.g., wind). Thus, flushing time calculations are
usually based on average conditions of tidal range and freshwater inflows,
with wind effects neglected.
The Fraction of Fresh Water Method for flushing time calculation is based
upon observations of estuarine salinities:
where F	=	flushing time in tidal cycles,
S	=	salinity of ocean water, and
S	=	mean estuarine salinity,
The tidal prism method for flushing time calculation considers the system
as one unit with tidal exchange being the dominant process:

VL + P
where F = flushing time in tidal cycles,
V, = low tide volume of the estuary, and
P = tidal prism volume (volume between low and high tides).
The Tidal Prism technique was further modified by Ketchum (1951) to segment
the estuary into lengths defined by the maximum excursion of a particle of
water during a tidal cycle. This technique can now include a freshwater
- i:
VL1 + "i
where F	=	flushing time in tidal cycles,
1	=	segment number,
n	=	number of segments
V, .	=	low tide volume in segment i, and
P^	=	tidal prism volume in segment.
Riverine Inflow is accounted for by setting the upstream length equal to
the river velocity multiplied by the tidal period, and setting:
P0 = QfT	(10)
where Prt = tidal prism volume in upstream segment,
-eshwater fit
idal period.
[jf = freshwater flow, and
Tt = ti<
Finally, the replacement time technique is based upon estuarine geometry
and longitudinal dispersion:
tR = 0.4 L2/El	(11)
where tR = replacement time,
L = length of estuary, and
El = longitudinal dispersion coefficient.

This technique requires knowledge of a longitudinal dispersion coefficient,
E, , which may not be known from direct estuarine measurements. A coeffici-
ent based upon measured data from a similar estuary may be
Table 11-4 for typical values in a number of U.S. estuaries)
estimated from empirical relationships, such as the one
Harleman (1964):
assumed (see
or it may be
reported by
EL = 77 n u R
or Harleman (1971):
E. = 100 n u_av R
L	max
longitudinal dispersion coefficient (ft /sec],
Manning's roughness coefficient (0.028-0.035, typically),
velocity (ft/sec),
maximum tidal velocity, and
hydraulic radius = A/P
where A = cross sectional area,
P = wetted perimeter.
Desktop Calculations of Pollutant Concentrations
Classification and characterization are means of identifying estuarine
types and their major processes as a basis for comparison with reference
estuaries. There are some desktop methods for calculating ambient water
quality for defined pollutant loading conditions which can provide further
insight into system response for use attainability evaluations.
These techniques usually assume uniform geometry, a well-mixed system, and
net freshwater driven flows. There are essentially two types of desktop
calculations for ambient water quality evaluations -- mixed tank analyses
and simple analytic solutions to the governing equations.
Under the first approach, the pollutant discharge is continuously mixed
with an inflowing river, or else at a point along the estuary. Solutions
at steady-state are well-known (Mills et al., 1982). For a river borne
pollutant inflow, the steady-state concentration for a conservative
pollutant may be calculated as follows:
Ti Qf

TABLE 11-4
Delaware River (DE/NJ)
Hudson River (NY)
East River (NY)
Cooper River (SC)
Savannah River (GA, SC)
Lower Raritan River (NJ)
South River (NJ)
Houston Ship Channel (TX)
Cape Fear River (NC)
Potomac River (MD/VA)
Cotnpton Creek (NJ)
Wappinger and Fishkill Creek (NY)
San Francisco Bay (CAj:
Southern Arm
Northern Arm
SOURCE: From Mills et al. (1982).
River Flow	Dispersion	Coefficents
(cfs)	(m2/sec)	(ft2/sec)
2500	150	1600
5000	600	6500
0	300	3250
10000	900	9700
7000	300-600	3250-6500
150	150	1600
23	150	1600
900	800	8700
1000	60-300	650-3250
550	30-300	325-3250
10	30	325
2	15-30	160-325
18-180	200-2000
46-1800	500-20000

where C . =	pollutant concentration in segment i,
T? =	flushing time for segment i,
Q- =	freshwater flow, and
=	water volume at segment i.
For a direct discharge along the estuary, the concentration of a
conservative pollutant at any section downstream is given by (Dyer 1973):
and at a section upstream:
where C =
C =
Qp =
ST =
subscript x -
subscript o -
subscript s -
inflow concentration,
inflow rate,
fraction of freshwater in segment,
river flow,
sal i ni ty,
denotes distance downstream,
denotes point of injection, and
denotes ocean salinity.
A refinement to the above desktop methods involve calculations for noncon-
servative pollutants. The usual approach is to rely upon a first order
decay relationship:
ct =
where Ct = concentration at time t,
C = initial concentration, and
kj - decay or reaction rate at temperature T.
The decay rate, k, is often expressed as a function of water temperature,
based upon the departure from a standard temperature (usually 20C):

T-20	, 
kT = k20 0	(18)
where k9n = decay or reaction rate at 20C, and
= constant (1.03-1.04).
The final" pollutant concentration is then calculated by applying a first-
order .decay to the dilution concentration given from Equations (14)-(16),
based on an estimate of travel time to the cross-section of interest.
The second approach is to greatly simplify the governing mass transport
equation, and derive a closed-form solution which can be evaluated using a
hand-held calculator, for continuous, discrete discharges of either con-
servative or non-conservative pollutants (Mills et al., 1982). From the
basic simplified equation for a continuous discharge of a nonconservative

EL " kc
the following solution can be readily derived:
cx =
co e*P

concentration at distance x (x is positive downstream, and
negative upstream)
initial concentration,
mean velocity,
longitudinal dispersion coefficient, and
decay rate.
in the upstream and downstream directions, respectively. Again, dispersion
coefficients, if not directly known, can be estimated from similar
estuaries, or from empirical formulas, such as those given in Equations
(12) and (13).
For multiple pollutant discharges, the resulting concentration curves for
each source may be superimposed to give a final composite profile along the
estuary (Figure 11-9).
Finally, Equation (20) can be used to estimate the length of salinity
intrusion by using salt as the constituent and assuming cross-sectional
homogeneity and an ocean salinity of 35 ppt (Stommel "1953):

Figure 11-9 Pattern of Recent Changes in the Distribution of Submerged Aquatic Vegetation (SAV)
in the Chesapeake Bay: 1950-1980. Arrows Indicate Former to Present Limits. Solid
Arrows Indicate Areas Where Eelgrass (Zostera Marina) Dominated. Open Arrows Indicate
Other SAV Species.
I frnnn II	PPfl Phoc a noa lft Rav PrftnMm. 1QR2}

3.5554 A E,
x =
where x =	length of intrusion from ocean to 1 ppt isohaline,
A =	cross-sectional area of estuary,
E. =	longitudinal dispersion coefficient, and
Q^ =	freshwater inflow rate.
Such a desktop evaluation of salinity intrusion can be used to relate
changes in freshwater inflow to use attainability within the upper estuary.
Other Desktop Evaluations for Use Attainability Assessments
The most common desktop evaluations of use attainability within estuaries
are statistical analyses of water quality monitoring data to determine the
frequency of delation of criteria for the-designated aquatic use. Statis-
tical evaluations of contraventions of water quality criteria should
consider the confidence intervals for the number of violations that are
attributable to random variations (rather than actual water quality
deterioration). For example, consider an estuary monitoring station with
12 dissolved oxygen (DO) observations per year (i.e., a single slackwater
sample each month) with a standard of 5 mg/1 DO. If statistical analyses
of the DO observations indicate that the upper and lower confidence limits
for the frequency of random violations of the 5 mg/1 DO standard cover a
range of 1 to 4 violations per year, a regulatory agency should be cautious
1n deciding whether actual use impairment has occurred unless more than 4
violations are observed annually.
In addition to the State water quality standard values, both quantitative
and qualitative measures should be considered for relationships between
water quality criteria and use attainment. Quantitative measures include
parametric statistical tests (i.e., assume normal frequency distribution)
such as correlation analyses and simple and multiple regression analyses,
as well as nonparametric statistical tests (i.e., distribution-free) such
as the Spearman and Kendall correlation analysis. These quantitative tests
might involve relating water quality indicators (e.g., DO, chlorophyll-a)
to use attainability indicators such as juvenile index data (numbers per
haul) for different finfish or commercial landings data (tons) for selected
fisheries. Qualitative measures include graphical displays of historical
trends in water quality and use attainment. For example, a map showing the
areas which have experienced a decline in bottom DO conditions during the
past 25 years could be overlaid on a map showing areas which experienced a
decline in oyster beds over the same period. Another example, which proved
to be very persuasive in the recent development of the U.S. EPA Chesapeake
Bay management program (U.S. EPA Chesapeake Bay Program, 1982), is
described in Figures II-9 through 11-12. Figures II-9 and 11-10 illustrate
the decline in submerged aquatic vegetation (SAV) in Chesapeake Bay during
the past three decades. Figures 11-11 and 11-12 illustrate changes in
nutrient enrichment within Chesapeake Bay over the same period. The water
quality index plotted in Figure 11-12 is based on changes in the concen-
trations of both nitrogen and phosphorus. As may be seen, the areas of

Figure 11-10 Sections of Chesapeake Bay Where Submerged Aquatic Vegetation (SAV) has
Experienced the Greatest Decline: 1950-1980
(from U.S. EPA Chesapeake Bay Program, 1982)

FtiOlPnOAuS ihoos
j/ ) mcooUngkuidt
j j O*cjailno *
| | Nokcndi

|" i<|ui'e ll-H I'hosplionis
( f mm N. *>.
HI iNacCH MttfOS
CltlSAf(A*(  *
,111(1 NitrcMjen Trends in Chesapeake llay: 1950-19H0
I I'A < tm 1 s^cr H.t/ Procjrani, 1982)

Degrading qualify
Improving qualify
No trend
Figure 11-12.
Water Quality Trends in Chesapeake Bay. If either N or P trends
(from Figure 11-11) are increasing, then the overall -water quality
is said to be degrading.

"degrading quality" in Figure 11-12 typically correspond to areas where
submerged aquatic vegetation has experienced the greatest decline. Based
on these types of qualitative comparisons and quantitative evaluations, the
U.S. EPA Chesapeake Bay Program has secured considerable State, Federal,
and Regional support for more aggressive water quality management efforts
to protect Chesapeake Bay. Key to making decisions is the presentation of
quantitative data as well as qualitative information.
In developing quantitative and qualitative measures for relationships
between water quality and use attainability, care should be taken to
distinguish the Impacts of pollution discharges from the impacts of
non-water quality factors such as physical alterations of the system. For
example, in some estuaries, dredging/spoil disposal activities associated
with the construction and maintenance of ship navigation channels and
harbors may have contributed to use impairment over the years. Among the
potential impacts of channel dredging is the reduction in the coverage of
SAY's. Therefore, in order to minimize interferences from dredging/spoil
disposal, analyses of water quality and use impairment for certain
fisheries (e.g., shellfish) and SAV habitats should be based upon periods
which do not include major dredging/spoil disposal operations. Another
example of physical alterations which should be accounted for in any trend
analyses is poor tidal flushing resulting from the construction of bridges
and causeways. Potential contributions of extreme meteorologic conditions
(e.g., hurricanes, air temperature) to use impairment should also be
consi dered.
If it 1s determined that some estuary segments exhibit use attainment
although violations .of water quality criteria occur, the development of
site-specific water quality criteria should be considered. Development of
site-specific criteria is a method for taking unique local conditions into
account. In the case of the water quality indicators (i.e., non-toxicants)
being considered in this guidance manual, a potential application of site-
specific criteria could be the establishment of temporal dimensions for
water quality criteria to restrict use attainment requirements to certain
seasons (i.e., in the event that year-round conformance with the water
quality criteria is not required to protect the viability of the designated
water use).
Computer Modeling Techniques for Use Attainability Evaluations
For many estuaries, field data on circulation, salinity, and chemical
parameters may be inadequate for desktop evaluations of use attainability.
In these cases, computer-based mathematical models can be used to expand
the data base and define causal relationships for use attainability
assessments. Specifically, there are three major areas in which computer
models of estuaries can contribute to use attainability evaluations:
1. Applications of hydrodynamic and mass transport models can expand
physical parameter data bases (i.e., circulation, salinity) in
order to identify aquatic use segments and to determine whether
physical characteristics are adequate for use attainment.

2.	Applications of water quality models can expand chemical parameter
(i.e., water quality) data bases in order to determine whether
ambient water quality conditions are adequate for use attainment.
3.	In cases where use impairment is noted despite acceptable physical
characteristics, applications of water quality models can identify
the causes of use impairment and alternative control measures that
promise use attainment.
The major problem facing the engineer or scientist performing the evalua-
tion is to select the most appropriate numerical model for a given study.
Such a selection process must be based on a consideration of system
geometry, physical and chemical processes of importance, and the temporal
and spatial scales at which the evaluation is being conducted.
Previously discussed were some of the simplifications that can be made to
reduce the conceptual complexity of an estuary from its inherently three-
dimensional nature. Unfortunately, few quantitative measures exist to
define precisely how such determinations should be made. Most criteria for
selecting the most appropriate mathematical modeling approach are based on
"intuitive judgment" or "experience" with few comparative indices, such as
stratification diagrams and numbers, to make the selection less arbitrary.
One particular problem that needs to be addressed is the selection of
steady-state versus dynamic approaches to estuarine modeling. Again,
intuition leads one to accept that steady-state approaches are fine for
rivers or. river-flow dominated systems, such as the upper 50-miles of the
Potomac River estuary near Washington, D.C. However, for areas further
downstream in the estuary where the river flow is less dominant particu-
larly in the dry season, one would intuitively consider using a dynamic
approach. The question then is how to formulate a criterion for choosing
between steady-state and dynamic modeling approaches. The governing
parameters in the selection criteria might be expected to be some com-
bination of freshwater inflow, tidal prism volume, density variations, and
tidal period, perhaps in the form of the estuary number, En, given by
Equation (7) or some other "number." A comparative study of various
approaches at differing estuary numbers, EQ, might lead to an empirical
formulation of a useful criterion for moael selection, similar to the
stratification diagram.
Once the appropriate simplifying assumptions have been made, the type of
model needed can be determined. There are several model classifications
that could be utilized for selection purposes. A four level scheme was
used by Ambrose et al. (1981) to classify and compare a number of estuarine
receiving water models. The recommended model classification scheme is as
Level 1
Level 2
Level 3
Level 4
-	desktop methodologies,
-	steady-state or tidally averaged models
-	one-dimensional or quasi-two-dimensional real time models,
-	two-dimensional or three-dimensional real time models.

Within each of the four levels, a number of numerical models are listed
(Ambrose et al. 1981) and their utility for problem solving is discussed.
In actuality, however, there are many more categories, which are sub-
divisions of the levels suggested by Ambrose et al. (1981). These are
summarized in Table 11 -5 and discussed below, except Level 1 which was
previously discussed.
Within Level 2, there are two subdivisions: one-dimensional steady-state
models, and two-layer steady-state models. One-dimensional steady-state
models assume that the hydraulics are driven entirely by a constant river
Inflow to the estuary or by net non-tidal (tidally averaged) flow. Con-
ditions are assumed to be uniform over the cross-section, and the effects
of Coriolis, wind, tidal, and stratification are neglected. Examples in
this category are QUAL II (Roesner et al., 1981) and the WASP models
(DiToro et al. 1981).
Two-layer (hydraulic) steady-state models are a simple, but fairly
significant extension beyond the one-layer models, in that the advective
transport can be resolved to allow for layered residual flow as in the
James River. O'Connor et al . (1983) developed such a model to study the
fate of Kepone in the James River, in which the net river flow could be
specified in the top layer, and the net upstream density-driven flow
specified in the lower hydraulic layer. In addition, this model has two1
sediment layers, one fluid and one fixed, with exchanges between all
In Level 3, models can be subdivided into two categories: one-dimensional
real time, and quasi-two-dimensional real time. The category of one-
dimensional real-time models has an advantage over steady-state models in
that the velocity field simulation can be completely dynamic, allowing
tides, wind, friction, variable freshwater inflows, and longitudinal
density variations to be Included. Again, the estuary is assumed to be
cross-sectionally homogeneous.
Quasi-two-dimensional real-time models are an improvement on the
one-dimensional real-time representation in that they allow branching
systems to be simulated. In addition, the link-node models (such as DEM
and RECEIV) can be configured to approximate a two-dimensional horizontal
geometry, thus allowing lateral variations to be included in the system
evaluation. A very popul ar-model in both these Level 3 categories is the
Dynamic Estuary Model (DEM) which represents the geometry with a branching
link-node network (Genet et al., 1974). This model is probably the most
versatile of its kind and has been applied to numerous estuarine systems,
bays, and harbors throughout the world. It contains a hydrodynamic
program, DYNHYD, or DYNTRAN (Walton et al., 1983) in its density driven
form, and a compatible water quality program, DYNQUAL, which can simulate
up to 25 water quality constituents, including four trophic levels.
There are a variety of categories that might be considered in Level 4.
Many two-dimensional, vertically-integrated, finite-difference hydrodynamic
programs exist. There are, however, relatively few that contain a water
quality program that simulates constituents other than salinity and/or
temperature (Blumberg, 1975; Hamilton, 1975; Elliot, 1976). These are real
time models, assuming only vertical homogeneity (Coriolis effects are now

1-D, steady-state
1-D real time
Quasi 2-D
real time
2-D, finite-difference
vertical Integrated
Uniform flows
River flows
River flows
Residual upstream
Longitudinal and
vertical variability
Tides, wind, river
flows, friction
Tides, wind, river
flows, friction
Longitudinal and
lateral variability
Tides, wind, river
flows, friction
Longitudinal and
lateral variability
Wind, Corlolls,
friction, tide
Lateral and vertical
Wind, Corlolls,
friction, tide
Lateral and vertical
Wind, Corlolls,
friction, tides
Lateral variations
Lateral and vertical
Corlolls, lateral
momentum transfer
Vertical variations
Vertical variations
See text
O'Connor et al.
Ross and Jerkins
2-D, finite-element
vertically Integrated
2-D, finite-difference
laterally Integrated
Tides, wind, river
flows, friction
Corlol Is
Longitudinal and
lateral variability
Tides, wind, river
flow, friction
Corlol 1 s
Longitudinal and
vertical variability
All physical processes
Vertical variations
Lateral variations
Chen (1978)
Leendertse et al,

included). An example of a water quality model in this category is the
hydrodynamic and water quality model developed by Ross and Jerkins (1983)
which has been extensively applied to Tampa Bay.
Similar to the above category are the two-dimensional, vertically-
integrated, finite-element models. The physical process and simplifica-
tions are identical. The difference is that the geometry is represented as
a series of elements (usually triangles) which can better represent complex
coastlines. Examples of models in this category are the CAFE 1/0ISPER1
hydrodynamic models (Wang and Connor 1975; Leimkuhler 1974), the Chesapeake
Bay Circulation Model, CBCM (Walton et al., 1983), and a water quality
model developed by Chen (1978). The first two models can simulate only
mass transport of a non-conservative constituent, whereas Chen's model is
capable of representing most major water quality processes. CBCM has the
additional advantages of a three-dimensional form and the capability to
link 1-2 or 2-3-dimensional models to treat tributaries from a main bay or
subgrid scale cuts in a main bay which cannot be resolved adequately at the
horizontal spatial scale.
There are a number of two-dimensional, 1aterally-averaged models (longi-
tudinal and vertical transport simulations) that treat mass transport of
salt and temperature, but very few that include nonconservative constit-
uents or water quality routines. While models in this category assume
lateral homogeneity and neglect Coriolis effects, they can represent
vertical stratification although for numerical reasons, care should be
taken in defining vertical layers to represent the saltwater/freshwater
.interface of high stratified systems. The tributary submodels of CBCM
(Walton et al., 1983) are included in this category.
Last is the category of three-dimensional, finite-difference and finite-
element models. These models allow all physical processes to be included,
although many were developed for systems of constant salinity (lakes or
oceans) "which cannot simulate stratification processes. Models in.this
category include CBCM (Walton et al. 1983) and the models of Leendertse et
al. (1973) which simulate hydrodynamics and the transport of salt, tem-
perature, and other conservative constituents.
Sample Applications of Estuary Models
Delineation of Aquatic Use Segments. Figure 11 -7 illustrates the use of
measured data on physical parameters to delineate homogeneous aquatic use
segments in Chesapeake Bay. For many estuaries, the measured data on
circulation and salinity will not have sufficient spatial and temporal
coverage to permit a comprehensive analysis of use attainability zones. In
cases where the measured data base is inadequate, computer models can be
used to expand the physical parameter data bases for segmentation of the
Figure 11-13 illustrates the use of model projections for Tampa Bay,
located on the Gulf Coast of central Florida, to delineate relatively
homogeneous segments for use attainability evaluations (Camp Dresser &
McKee, Inc. 1983). Tampa Bay is considerably smaller and shallower than
Chesapeake Bay, with a surface area (approx. 350 sq. mi.) that is less than
10 percent of the Maryland/Virginia estuary's (approx. 5^00 sq. mi."

Figure 11-13. Map of Tampa Bay lowing Sample Estuary Segments
(A through N) and Net Current Velocities for a
Single Tidal Cycle (from Camp Dresser and McKee 1983)

including tributaries). The Tampa Bay estuary exhibits extremely diverse
and abundant marine life which has been attributed to the geographic
position of the estuary between temperate and subtropical waters. As a
result of Tampa Bay's location, winter water temperatures rarely fall to
levels which could kill tropical organisms and summer water temperatures
are moderate enough to be tolerated by many of the temperate species.
Another contributing factor to the diversity and abundance of Tampa Bay
marine life is that salinity is typically in the range 25-35 ppt over most
of the estuary, without the wide fluctuations and significant vertical
stratification that characterize many other estuaries. As a result of the
stability of the salinity regime, many ocean species can coexist with
typical estuarine species.
Tampa Bay's salinity regime is also much different from Chesapeake Bay's.
Whereas extensive areas in Chesapeake Bay exhibit vertical stratification,
Tampa Bay is very well-mixed vertically due in large part to its relatively
shallow mean depth (i.e., relationship of storage volume to surface area).
Unlike Chesapeake Bay where circulation and mass transport must be evalu-
ated in the vertical as well as horizontal and longitudinal directions,
only the horizontal and longitudinal directions need to be considered for
Tampa Bay evaluations. Therefore, the sample analysis of Tampa Bay is a
good example of a segmentation approach to an estuary where the use is not
significantly influenced by vertical - stratification. It is also a good
example of how an estuary circulation model can be used to segment an
estuary for use attainability analyses.
The estuary segment boundaries shown in Figure 11-13 have been delineated
on a map of Tampa Bay showing circulation model projections of net current
velocities (i.e., magnitude and direction) for a single tidal cycle. The
model projections are based upon a two-dimensional circulation model
(horizontal and longitudinal directions) which had previously been
calibrated to measured current velocity and tidal elevation data for Tampa
Bay (Ross and Jerkins, 1978). The use of the model expanded the available
circulation data base from a limited number of gaging stations to
comprehensive coverage of the entire Bay. One of the most important
factors in subdividing the Tampa Bay estuary system into relatively
homogeneous subunits is the ship navigation channel extending from the
mouth of the Bay to the vicinity of Interbay Peninsula with branches
extending into Hillsborough Bay (segment D) and into the lower end of Old
Tampa Bay (segment C). As may be seen from the convergence of velocity
vectors in the vicinity of the navigation channel, there tends to be
relatively little mixing between waters on either side of the Main Bay
channel. Therefore in Figure 11-13, the navigation channel and the
adjoining dredge spoil areas serve as the approximate boundary between seg-
ments H and I and between segments F and G. Each of these segments appears
to be relatively isolated from its counterpart on the opposite side of the
navigation trench before mixing occurs in the vicinity of the navigation
channel, thereby justifying the designation of each as a separate segment.
Water movement is also somewhat isolated on approximately either side of
the navigation channel branches extending into Hillsborough Bay and the
lower end of Old Tampa Bay. However, since net current velocities tend to
converge a short distance south of the two ship channel branches, the

boundaries between segments E and F and E and G in Figure 11-13 depart
somewhat from the navigation trench.
Another circulation factor considered in the delineation of estuary
segments is the impact of causeways and bridges on tidal flushing. Based
upon the circulation patterns shown in Figure 11-13, it seems appropriate
to assign separate segment designations (A, B, and C) to the areas above
the three bridge crossings in Old Tampa Bay: Courtney Campbell Causeway
(boundary .between segments A and B), Howard Franklin Bridge (boundary
between segments B and C) and Gandy Bridge (boundary between segments C and
F). Likewise, McKay Bay (segment K), which is separated from Hillsborough
Bay by the 22nd Street Causeway, also merits a separate segment desig-
A final circulation factor in the open bay is the location of net rotary
currents (indicated by circles in Figure 11-13) which are called "gyres."
The gyres result from water moving back and forth with the tides, while
following a net circular path. Gyres can have a significant effect on
flushing times, since waters caught in the gyres typically exhibit much
higher residence times than waters which are not affected by these areas of
net rotary currents. The use of the main ship channel and causeway/bridge
crossings as segment boundaries in Figure 11-13 has generally isolated the
major gyres or groups of gyres. Further subdivision of the Hillsborough
Bay segment (0) to isolate the waters on the eastern and western sides of
the ship channel (which bisects segment D) does not appear to be warranted
because of the two gyres in the middle section of the Bay and the gyre in
lower Bay. In other words, the gyres in Hillsborough Bay are indicative of
an irregular circulation pattern that seems to mix waters on both sides of
the ship channel. Likewise, the gyres within segment B are indicative of a
circular mixing pattern throughout the segment which suggests that further
subdivision into eastern and western sections is not justified.
The segment network in Figure 11-13 also maintains relatively homogeneous
salinity levels within each segment. The greatest longitudinal variations
in salinity occur in segments F and G which exhibit 3-5 ppt increases in
average annual values between the upper and lower ends of the segment. If
these longitudinal variations in salinity will result in significant
differences in the biological community, further subdivision of segments F
and G should be considered.
Figure 11-13 also shows five separate segments for significant embayments:
Safety Harbor (J), McKay Bay (K), Alafia River (L), Hillsborough River (M),
and Little Manatee River (N). The latter three represent the tidal sec-
tions of the indicated river. In addition to these five embayments there
may be other inlets which should be separated from Tampa Bay segments for
separate use attainability studies.
In summary, the network shown in Figure 11-13 illustrates how hydrodynamic
and salinity data produced by an estuary model can be used to segment the
Tampa Bay system. In addition to the type of hydrodynamic data shown in
Figure 11-13, the estuary model can be used for "particle tracer" studies
that can further address issues such as mixing of waters on either side of
the ship channel and the impacts of gyres.

Evaluation of Use Attainment Based Upon Ambient Water Quality Data. It is
often the case that the measured ambient water quality data base is inade-
quate from temporal and/or spatial standpoints for a definitive assessment
of use attainment.
An example of temporal limitations is an ambient water quality data base
that suffers from a small sample size (e.g., 6-12 slackwater observations
at each station per year), thereby resulting in extremely wide confidence
intervals for the number of violations of standards and criteria that are
attributable to random variations (rather than actual water quality
Another example of temporal limitations is an observed water quality
data base that is restricted to a single daytime observation on each
sampling day. This type of data base may not provide any insights into
diurnal variations in DO which can result in use impairment, since
nighttime DO's can be significantly lower than daytime values due to
diurnal variations in algal production/respiration.
An example of spatial limitations in the measured water quality data base
1s inadequate coverage of longitudinal and/or horizontal variations in
water quality. Adequate longitudinal coverage is required in all estuaries
to assess the significance and spatial extent of maximum and minimum con-
centrations 1n the estuary. Adequate horizontal coverage is required in
relatively wide estuaries where horizontal transport processes are
Another example of spatial limitations would be the collection of surface
water samples only within an estuary which exhibits extensive areas of
vertical stratification. The lack of bottom water samples may prevent an
adequate assessment of use attainment, 'since potential depressions of
bottom water DO levels cannot be evaluated.
In cases where the measured water quality data base is inadequate from
either temporal or spatial standpoints, an estuary model should be used to
expand the data base for use attainability evaluations. The model must
first be calibrated with the available measured data base to demonstrate
that its representation of the prototype produces water quality statistics
that are not significantly different from the measured statistics. The
reliability of the estuary model projections depends upon the amount and
type of measured data available for model calibration. If the measured
data base provides^ reasonably good coverage of spatial and temporal (e.g.,
both short-term and long-term) variations in water quality, projections by
a model calibrated to this data base should be quite reliable in a statis-
tical sense. If the measured data base used for calibration is quite
limited, estuary model projections will be less reliable; however, the
application of an appropriate model to an estuary with limited measured
data can still provide significant insights for use attainability eval-
uations and considerable guidance for future estuary monitoring programs.
To illustrate the use of an estuary model for use attainment evaluations, a
sample application of a one-dimensional (1-D) model to Naples Bay, Florida
is described below (Camp Dresser & McKee, Inc. 1983). Naples Bay (see
Figure 11-14) is a rather small estuary (less than 1.5 sq. mi. surface

jCL den gate
Figure 11-14. Node and Channel Network for the Naples Bay DEM
model.	H-50

area) located on the Gulf Coast of southeastern Florida. The City of
Naples' municipal wastewater treatment plant (secondary treatment) which
discharges to the Gordon River portion of the Naples Bay estuary, is the
only major point source of pollution. This sample application illustrates
the impacts of an 8.0 million gallons per day (mgd) discharge from the
Naples wastewater treatment plant. Nonpoint pollution loadings are con-
tributed by rainfall runoff and groundwater recharge from a 155 sq. mi.
drainage area, the majority of which discharges to the estuary at the
uppermost point in the system (node no. 1 in Figure 11-14). The Gulf of
Mexico boundary condition (introduced at node no. 29 in Figure 11-14) also
contributes nutrients and other constituents to the lower Bay. Since the
Naples Bay system is a relatively narrow and shallow estuary, it was
assumed that a 1-D model which only represents longitudinal transport would
be adequate for this water quality evaluation (I.e., horizontal and
vertical gradients are neglected). A schematic of the 1-D representation
of the Naples Bay system with the Dynamic Estuary Model (DEM) is shown in
Figure 11-14.
As indicated in the earlier section on modeling techniques, the DEM model
(Genet et al., 1974) applied to Naples Bay is one of the most widely used
estuary models in the U.S. DEM provides a representation of intertidal
hydrodynamics and mass transport with computation intervals which are
typically less than one hour. The model simulates 1-D flow, mass trans-
port, and water quality processes in a network of channels connected by
junctions called "nodes." As shown in Figure 11-14, the DEM model network
applied to Naples Bay consists of 29 nodes and 28 channels. This network
includes all the appropriate conveyance and storage features of the proto-
type system, including bifurcation around an island (between nodes 7 and
10), and the canal system adjacent to the main water body. Streamflows,
wastewater discharges, and associated pollutant loadings are added to the
system at the nodes. Based upon a set of motion equations solved for the
channels arid a set of continuity equations solved for the nodes, the hydro-
dynamic portion of the model calculates flows and velocities in the chan-
nels, and water surface elevations at the nodes. An accurate representation
of hydrodynamic processes within the system is developed to adequately
model mass transport and water quality processes.
The output from the hydrodynamic model becomes input to the water quality
model which calculates mass transport between nodes and calculates changes
in concentration due to physical, chemical and biological processes. Water
quality processes represented by this portion of the model include: mass
transport based upon advection and dispersion, BOD decay, nitrification,
algal productivity, benthic sources of pollutants, dissolved oxygen sources
and sinks, and fecal coliform die-off.
Following calibration and verification of the Naples Bay model with mea-
sured hydrodynamic and water quality data, the model was used to assess
estuary-wide water quality. Figure 11-15 shows the model projections of
wet season chlorophyl1-a (i.e., phytoplankton concentrations) for secondary
treatment operations which were in effect at the Naples wastewater treat-
ment plant. As indicated in an earlier section, chlorophyll-a is an
important indicator of estuary health for use attainability evaluations.

		x					X....V
11-15 Comparison of Simulated Average Daily Chlorophyl1-a in Main Stem of
Naples Bay Projected for Different Wastewater Discharge
Scenarios: "Worst Case" Wet Season Conditions

The chlorophyll-a simulations shown in Figure 11-15 represent "worst case"
water quality conditions at the start of the wet season (i.e., 4-month
period of significant rainfall and high streamflow). As may be seen from
the plot of "Secondary STP" conditions along the main stem of the Bay, the
combination of point and nonpoint source loadings of nitrogen and phosphor-
us under wet season conditions results in chlorophyll-a levels exceeding 50
ug/1 for almost 3.0 miles and maximum values on the order of 80 ug/1 for
about 1.0 mile. The volume-weighted mean chlorophyll-a (i.e., weighted by
the storage volume in each estuary segment) for the upper two miles (i.e.,
Gordon River) of the estuary is about 60 ug/1, while the volume-weighted
mean for the entire estuary is about 45 ug/1. These maximum and mean con-
centrations can be compared with state or regional water quality criteria
for local use attainability, evaluations. Additional model projections can
be developed for other wet season and dry season conditions to evaluate the
frequency of use impairment expressed in terms of ambient water quality.
Since chlorophyll-a impacts are primarily of interest in terms of associ-
ated impacts on DO, the estuary model can also be used to evaluate diurnal
DO impacts for use attainability assessments. Once chlorophyll-a and DO
relationships have been evaluated, the estuary model can be used to evalu-
ate nitrogen and phosphorus goals' that maintain chlorophyll-a at levels
ensuring use attainment.
Evaluations of Use Impairment Causes and Alternative Controls. Estuary
models ari probably most useful for management evaluations following a
determination of use impairment in certain sections of the estuary. Models
can be used to define the causes of impairment and to define the effect of
alternate controls on .attaining the use. Such analyses require the
development of causal relationships between pollution loadings, physical
modifications and the resulting changes in uses. It is very difficult to
develop such causal relationships from statistical analyses of measured
data. For example, regression equations can merely indicate that pollution
loadings and impairment of the uses appear to be correlated based upon the
measured data base. Such regression equations should not be interpreted as
definitive indications of cause-effect relationships. Evaluations of
cause-effect relationships require the use of a deterministic estuary
Evaluations of use impairment causes will typically focus on comparisons of
point and nonpoint source pollution impacts. The estuary model is well-
equipped to perform such evaluations because both point and nonpoint source
loadings can be "shut off" (i.e., deleted from the system) for evaluations
of relative contributions to use impairment. Applications of the Naples
Bay model will be used to illustrate how evaluations of cause-effect rela-
tionships can be performed. After analyses of the impacts of existing
secondary treatment operations at the 8.0 mgd wastewater treatment plant,
the .Naples Bay model was rerun with no wastewater discharges. For this
model run, the only sources of nutrients and other constituents were
nonpoint source flows from the Bay's 155 sq. mi. drainage area and ocean
boundary conditions at the mouth of the Bay. The resulting chlorophyll-a
projection for "worst case" wet season conditions are shown in Figure 11-15
as the "Zero STP Discharge" plot. As may be seen, the maximum chlorophyll-
a concentration is about 25 ug/1, with concentrations on the order of 15-25
ug/1 for about 5.0 miles. The chlorophyll-a concentrations for the "Zero
STP Discharge" condition are typically only 25-50 percent of the existing

"Secondary STP" levels for about 5.0 miles. Also, the location of the
maximum chlorophyll-a concentration is shifted about 1.0 mile further
downstream for the "Zero STP Discharge" condition. The mean volume-
weighted chlorophyll-a for the entire Bay is approximately 20 ug/1 which is
less than half of the "Secondary STP" mean. These evaluations suggest that
secondary effluent discharges from the wastewater treatment plant are the
major cause of relatively high chlorophyll-a levels under wet season
conditions. Approximately 50-55 ug/1 or about 70 percent of the peak
chlorophyll-a concentration (80 ug/1) and about 25 ug/1 or 55 percent of
systemwide volume-weighted mean concentration can be attributed to the
wastewater treatment plant.
Chlorophyll-a is a specific index of pliytoplankton biomass. Thus, assuming
that the chlorophyll-a levels associated with the "Secondary STP" condition
indicate use impairment, the estuary model provides a mechanism for eval-
uating the use attainability benefits of alternate controls. The Naples
Bay model was rerun with the 8.0 mgd discharge upgraded to advanced waste-
water treatment (AWT) levels. The simulated AWT upgrading involved
reducing total phosphorus effluent levels from 7.0 mg/1 to 0.5 mg/1 as P,
the achievement of almost total nitrification in comparison with less than
50 percent nitrification for secondary treatment conditions, and reducing
5-day biochemical oxygen demand (BOD) from 20 mg/1 to 5 mg/1. Nonpoint
source loadings and ocean boundary conditions were set at the same levels
as the "Secondary STP" model runs. As shown in Figure-11-15, the projected
chlorophyll-a concentrations for the "AWT" conditions are 20-30 percent
lower than'the "Secondary STP" levels for approximately a two mile section
that includes the maximum concentrations for both scenarios. The AWT
scenario's maximum concentrations of chlorophyll-a are on the order of
50-60 ug/1 for about 2.5 miles, while the volume-weighted mean concentra-
tion for the entire Bay system is about 40 ug/1. Even under AWT condi-
tions, the maximum chlorophyll-a levels for AWT conditions are still about
35 ug/1 greater than the maximum values for "Zero STP Discharge" condi-
The maximum and mean concentrations for AWT conditions can be compared with
water quality criteria to determine if this control measure can achieve use
attainment. If the projected chlorophyll-a reductions are not sufficient
to prevent use impairment, the model can be rerun to assess the use
attainability benefits of nonpoint source controls in addition to AWT
The bottom of most estuaries is a mix of sand, silt and mud that has been
transported and deposited by ocean currents or by freshwater sources.
Rocky areas may also be seen, particularly in the fjord-type estuary. None
of these substrate types are particularly hospitable to aquatic plants and
animals, which accounts in part for the paucity of species seen in an
Much of the estuarine substrate is in flux. The steady addition of new
bottom material, transported by currents, may smother existing communities
and hinder the establishment of new plants and animals. Currents may cause

a constant shifting of bottom sediment, further hindering the colonization
of species. Severe storms or flooding may also disrupt the bottom.
The sediment load introduced at the head of the estuary will be determined
by the types of terrain through which the river passes, and upon land use
practices which may encourage runoff and erosion. It is important to take
land use practices into consideration when examining the attainable uses of
the estuary. The heavier particles carried by a river will settle out
first when water velocity decreases at the head of the estuary. Smaller
particles do not readily settle and may be carried a considerable distance
Into the estuary before they settle to the bottom. The fines may never
settle and will contribute to the overall turbidity which is characteristic
of estuaries.
It is often difficult for plants to colonize estuaries because they may be
hindered by a lack of suitable anchorage points, and by the turbidity of
the water which restricts light penetration (McLusky, 1971). Attached
plant communities (macrophytes) develop in sheltered areas where silt and
mud accumulate. Plants which become established in these areas help to
slow prevailing currents, leading to further deposition of silt (Mann).
The growth of plants often keeps pace with rising sediment levels so that
over a long period of time substantial deposits of sediment and plant
material may be seen.
Attached plant communities, also known as submerged aquatic vegetation
(SAV), serve very important roles as habitat and as food source for much of
the biota of the estuary. Major estuary studies, including an intensive
years-long study of the Chesapeake Bay, have shown that the' health of SAV
communities serves as an important indicator of estuary health. Although
excess siltation may have some adverse effects on SAV, as discussed above,
this problem is minor compared to the effects of nutrient and toxics
loadings to the estuary. When SAV communities are adversely affected by
nutrients and/or toxics, the aquatic life uses of the estuary also will be
affected. The ecological role of SAV in the estuary will be discussed
further in Chapter III, and its importance to the study of attainable uses
in Chapter IV.
Sediment/substrate properties are important because such properties: (1)
determine the extent to which toxic compounds in sediments are available to
the biota; and (2) determine what types of plants and animals may become
established. The presence of a suitable substrate may not be sufficient,
however, since nutrient, DO, and/or toxics problems may cause the. demise
and prevent the reestablishment of desirable plants and animals. There-
fore, characterization of the substrate is important to a use attainability
study in order to understand what types of aquatic life should be expected
in a given area.
Tidal and freshwater wetlands adjacent to the estuary can serve as a buffer
to protect the estuary from external phenomena. This function may be
particularly important during wet weather periods when relatively high
streamflows discharge high loads of sediment and pollutants to the estuary.

The volume of sediment carried by streamflow during wet weather periods is
substantially greater than the amount transported into the estuary by
rivers and streams during dry weather periods. Such shock loads could
quickly smother plant and animal communities and jeopardize their survival.
Wetlands can serve an important function by protecting the estuary from
such shock loads. Because of the sinuous pattern of streams that flow
through the wetlands, and the high density of plants, water velocities will
be reduced enough to allow settlement of a substantial proportion of the
sediment load before it reaches the estuary. This simultaneously protects
the estuary and contributes to the maintenance of the wetlands.
The sediment load discharged by streamflow may be accompanied by nutrients
and other pollutants. Excessive loadings of nutrients such as nitrogen and
phosphorus may promote eutrophication and the growth of algal mats in the
estuary, which is undesirable from both aquatic use and aesthetic stand-
points. On the other hand, these nutrients are beneficial to the main-
tenance of plant life in the wetland.
Another important function of a wetland is to reduce peak streamflow dis-
charges into the estuary during wet weather periods. To the extent that
this peak flow attenuation prevents abrupt changes in salinity, the flora
and fauna of the estuary are protected. It has been common practice to
straighten existing channels and cut new channels in wetlands to speed
drainage and enable the use of wetlands for agriculture or other develop-
ment. Such channelization may diminish the protective functions of the
wetland and have an adverse impact on the health of the estuary.
While the wetland may help to withhold nutrients in the form of nitrogen
and phosphorus from the estuary, it serves as a major source of nutrients
In the form of detritus. A substantial portion of dead plant material in
the wetland is transported to the estuary as detritus. Detritus is a basic
fuel of the estuary, serving as the main source of nutrient for filter
feeders and many fish at the bottom of the food chain. The estuary is
highly productive, more so than the freshwater or marine environment,
because of this source of nutrients.
Since the alteration or destruction of wetlands may hold important impli-
cations for the health of the estuary, it is important during the course of
a water body survey to examine historical trends in the wetland acreage,
locations, and character!sties for clues which explain changes in the
estuary and its uses. The extent to which wetlands have been irreversibly
altered may establish bounds on the uses that might be expected. Converse-
ly, restoration of wetlands may provide some means of restoring uses pro-
vided that other conditions such as toxic or nutrient loadings are not a
problem, or some other irreversible change has not been made to the
There are two important sources of freshwater to the estuary-streamflow and
direct precipitation. In general, streamflow represents the greatestcon-
tribution to the estuary and direct precipitation the smallest.

The location of the salinity gradient in the river controlled estuary is to
a large extent an artifact of streamflow. The location of salinity iso-
concentration lines may change considerably, depending upon whether stream-
flow is high or low. This in turn may affect the biology of the estuary,
resulting in population shifts as biological species adjust to changes in
sal i ni ty.
Most species are able to survive within a range of salinity levels, and
therefore most aquatic uses may not be adversely affected by minor shifts
1n the salinity gradient. Most of the biota can also sustain temporary
extreme changes in salinity, either by flight or through some other mechan-
ism. For example, molluscs may be able to withstand temporary excursions
beyond their preferred salinity range by simply closing themselves off from
their environment. This is important to their survival since the adult is
unable to relocate in response to salinity changes. However, molluscs can-
not survive this way indefinitely.
Generally speaking, the response of a stream or estuary to rainfall events
depends upon the intensity of rainfall, the drainage area affected by the
rainfall and the size of the estuary. Movement of the salt front is depen-
dent upon tidal influences and freshwater flow to the estuary. Variations
in salinity generally follow seasonal patterns such that the salt front
will occur further down-estuary during a rainy season than during a dry
season. The salinity profile may also vary from day to day reflecting the
effect of individual rainfall events, but may also undergo major changes
due to extreme meteorological events.
The location of.the salt front in a small estuary may be easily displaced
but rapidly restored in response to a rainstorm, whereas the effect of the
same size storm on salinity distribution within a larger estuary may be
minor. For a large system, the contribution of a given storm may be only a
fraction of the overall freshwater flow and thus will have no appreciable
effect. For a small system the contribution of a given storm may be very
large compared to overall flow, and the system will respond accordingly.
A rapid increase in flow may have several deleterious effects on a small
estuary: (1) the salinity gradient changes drastically, placing severe
stress on non-motile species and forcing the migration of motile forms, (2)
a sediment and pollutant load which is too large to be captured by sur-
rounding wetlands may be transported into the estuary, and (3) the bottom
may be scoured in areas of high flow velocity, destroying floral ahd faunal
communities and existing, habitat, and eliminating the conditions that would
be required for replacement communities to become established.
Major shifts in salinity due to extreme changes in freshwater flow are not
uncommon. An excellent example is the impact of Hurricane Agnes on the
Chesapeake Bay in 1972.' The enormous and prolonged increase in freshwater
flow to the Bay shifted the salinity gradient many miles seaward and had a
devasting effect on the shellfish population. The flow was so great that
salinity levels did not return to normal for several months, a period far
longer than non-motile species would be able to survive such radical reduc-
tions in salinity. In addition, the enormous quantities of sediment deliv-
ered to the Bay by Hurricane Agnes exerted considerable stress on the Bay

Anthropogenic activity may also have a significant effect on salinity in an
estuary. When feeder streams are used as sources of public water supply
and the withdrawals are not returned, freshwater flow to the estuary will
be reduced, and the salt wedge found further up the estuary. If the water
is returned, usually in the form of wastewater effluent, the salinity grad-
ient of the estuary may not be affected although other problems might occur
which are attributable to nutrients and other pollutants in the wastewater.
Even when there is no appreciable change in annual freshwater flow or qual-
ity due to water supply uses, the salinity profile may still be affected by
the way in which dams along the river are operated. Flood control dams may
result in controlled discharges to the estuary rather than relatively short
but massive discharge during high flow periods. A dam which is operated so
as to impound water for adequate public water supply during low-flow per-
iods may severely alter the pattern of freshwater flow to the estuary. Al-
though annual input to the estuary may remain unchanged, seasonal changes
may have a significant impact on the estuary and its biota.
The discussion of hydrology, meteorology and the effect of hydraulic struc-
tures in this section provides only an overview of their possible effects
on the health of an estuary. Hydrologic impacts will depend upon the uni-
que physical characteristics of the estuary and its feeder streams, in-
cluding structural activity that may have changed flow characteristics to
the estuary. Extreme rainfall events are particularly important because
they may result in physical damage to wetlands and to the estuarine sub-
strate, and may subject the biota to abnormally low salinities as the salt
wedge is driven seaward. Extreme periods of drought may also have an ad-
verse impact on the estuary. The operation of hydraulic structures  dams
and diversions --can significantly alter the characteristics and the uses
of an estuary. Clearly, these characteristics must be taken into account
in determining the attainable uses of the water body.-

Salinity, light penetration and substrate composition are the most critical
factors to the distribution and survival of plant and animal communities in
an estuary. This Chapter begins with an overview of the physical phenomena
and biological adaptations which influence the colonization of the estuary.
Following this, specific information is presented on Estuarine Plankton
(phytoplankton and zooplankton), Estuarine Benthos (infaunal forms,
crustaceans and molluscs), Submerged Aquatic Vegetation, and Estuarine
F1sh. There is also a short discussion of measures of biological health
and diversity. This last subject is presented in much greater detail in
the Technical Support Manual (U.S. EPA, November 1983).
The information in this Chapter (and its associated Appendices) has been
compiled to provide an overview of the types of habitat, ranges of
salinity, and life cycle and other requirements of plants and animals one
might expect to find in an" estuary, as well as analyses that might be
performed to characterize the biota of the system.
With this information having.been presented as a base, discussion in
Chapter IV will be directed towards how the biological, chemical and
physical data descriptive of the estuary may be synthesized into an
assessment of the present and potential uses of the estuary.
The estuarine environment is characterized by variations in circulation,
salinity, temperature and dissolved oxygen supply. Due to differences in
density, the water is generally fresher near the surface and more saline
toward the bottom. Colonizing plants and animals must be able to withstand
the fluctuating conditions in estuaries. Rooted plants need a stable
substrate to colonize an area. Once established, the roots of aquatic
vegetation help to stabilize the sediment surface, and the stems interfere
with and reduce local currents so that more material may be deposited.
Thus, small hummocks become larger beds as the plants extend their range.
The depth to which attached plants may become established is limited by
turbidity, since they require light for photosynthesis. Estuaries are
typically turbid because of large quantities of detritus and silt
contributed by surroundfng marshes and rivers-. Algal growths may also
hinder the penetration of light. If too much light is withheld from the
lower depths, animals cannot rely heavily on visual cues for habitat
selection, feeding, or in finding a mate.
Estuarine animals are recruited from three major sources: the sea,
freshwater environments, and the land. Animals of the marine component
have been most successful in colonizing estuarine systems, although the

extent to which they penetrate the environment varies (Green 1968).
Estuarine animals that belong to groups prevalent in freshwater habitats
are presumed to have originated there. Such species comprise the fresh-
water component. The invasion of estuaries from the land has been
accomplished mainly by arthropods.
When animals encounter stressful conditions in an estuary, they have two
alternatives: they can migrate to an area where more suitable conditions
exist, or if sedentary or sessile they can respond by sealing themselves
inside a shell, or by retreating into a burrow.
Most stenohaline marine animals can survive in salinities as low as
10-12 ppt by allowing the internal environment (blood, cells, etc.) to
become osmotlcally similar to the surrounding water (McLusky 1981). Such
"conformers" often change their body volume. In contrast oligohaline
animals actively regulate their internal salt concentration. They do so by
active transport of sodium and potassium ions (Na , K ). Osmoregulation
relies on several possible physiological adaptations. Reduced surface
permeability helps minimize osmotic flow of water and salts. In addition,
the animal's excretory organs serve to conserve idns or water needed for
Upper and lower tolerance limits define a range between which environmental
factors are suitable for life (zone of compatibility). The adaptations of
these tolerance limits are referred to as resistance adaptations. In
estuaries, the major environmental factors to which organisms must adjust
are periodic submersion and desiccation as well as fluctuating salinity,
temperature, and dissolved oxygen.
Vernberg (1983) notes several generalizations concerning the responses of
estuarine organisms to salinity: (1) those organisms living in estuaries
subjected to wide salinity fluctuations can withstand a wider range of
salinities than species that occur in high salinity estuaries; (2) inter-
tidal zone animals tend to tolerate wider ranges of salinities than do
subtidal and open-ocean organisms; (3) low intertidal species are less
tolerant of low salinities than are high intertidal ones; and (4) more
sessile animals are likely to be more tolerant of fluctuating salinities
than those organisms which are highly mobile and capable of migrating
during times of salinity stress. These generalizations reflect the
correlation of an organism's habitat to its tolerance. Some estuarine
animals are able to survive in adverse salinities, provided that the stress
is fluctuating, not constant. For example, initial mortalities of the
oyster drill (Urosalpinx cinerea) were very high when exposed to constant
low salinity values. However, little or no mortalities occurred during ten
days of exposure to low fluctuating, salinities. Tolerance limits may also
differ between larval and adult stages, as in the case of fiddler crabs
(lica pugilator). Adults are able to survive extended periods of 5 ppt
salinity, while larvae cannot tolerate salinities below 20 ppt (Vernberg
1983). The salinity in which they were spawned may also influence larval
Temperature also has an effect on salinity tolerances of organisms.
Generally, cold-water species can tolerate low salinities best at low
temperatures and tropical species can withstand low salinities best at high

temperatures. The previous thermal history of an organism influences its
resistance to temperature extremes. Acclimation to higher salinities can
also broaden an organism's zone of compatibility for temperature.
The transport of oxygenated surface water to the bottom is greatly in-
hibited when an estuary is stratified. In addition, the solubility of
oxygen in water is suppressed by salinity, so that estuarine DO levels at a
given temperature may not be as high as would be seen in freshwater. As a
consequence, many estuaries exhibit consistently low DO levels in the lower
part of the water column, and may become anoxic at the bottom. This con-
dition may be exacerbated by benthic DO demand. Many estuarine organisms
must be tolerant of low DO. Those that are able will leave to seek areas
of sufficient dissolved oxygen, while others (such as bivalves) will
respond by regulating metabolic activity to levels that can be supported by
the ambient DO concentration.
Intertidal organisms experience alternating periods of desiccation and
submersion. These animals, mainly molluscs, are able to resist desiccation
because of morphological characteristics that aid in controlling water
losses. Others burrow into the moist substrate to avoid prolonged exposure
to the air. Small animals with high ratios of surface area- to volume are
less, res-istant-to water loss than are larger organisms.
Estuaries are characterized by high productivity but low species diversity".
Several authors have noted decreased species diversity in estuaries when
compared to freshwater or marine systems (Green 1968, McLusky 1971, McLusky
1981, Haedrich 1983). Two major hypotheses explain the paucity of
estuarine species. The first explanation is that of physiological stress
caused by variable conditions in estuaries (McLusky 1981). Plants and
animals must be able to withstand considerable changes in salinity, DO and
temperature. In addition, because of tidal variation, they may be sub-
jected to periods of dessication. Variable salinities are especially
challenging to an organism's ability to osmoregulate. Because conditions
in estuaries are not stable, fewer species inhabit estuaries than inhabit
fresh or marine waters.
The second hypothesis explains decreased species diversity by the relative
youth of present-day estuaries (McLusky 1971, McLusky 1981, Haedrich 1983).
The estuaries that we see today probably did not exist several thousand
years ago. Since this is a short period relative to the same scale over
which speciation has taken place, few species have been able to adapt to
and colonize the estuarine system. An investigation by Allen and Horn
(1975) of several small estuarine systems in the United States revealed
tnat a small number of species (<5) comprised more than 75 percent of the
total number of individuals. Similarly, Haedrich (1983) noted that the
number of fish families characteristic of estuaries comprises only six
percent of the total number of families described.
Investigations of diversity in estuarine systems have employed the same
diversity indices that are commonly used in freshwater systems (see U.S.
EPA, 1983_b, Chapter IV-2). The Shannon-Wiener index is often employed in
conjunction with the two components that influence its value, a species

richness index and a measure of evenness (McErlean 1973, Allen and Horn
1975, Hoff and Ibara 1977).
Because seasonal changes are so marked in estuaries, the selected diversity
index should be sensitive to changes in species composition. Thus,
quantitative similarity coefficients and cluster analyses may be used to
determine the extent of similarity between samples. Such measures are
discussed, in Chapter IV-2 of the Technical Support Manual: Waterbody
Surveys and Assessments for Conducting Use Attainability Analyses (U.S.
EPA, 1983b).
An equal effort should be expended at each sampling station each time
sampling is done. The results of a fish fauna survey may be biased by the
sampling method employed. For example, the gear used (trawl, gill net,
trap net, seine), the mesh size and the area in which fishing occurs
determine the sizes, numbers and kinds of fish caught (McHugh 1967,
McErlean 1973). Sampling gear and technique are also important in benthic
and planktonic investigations. Because of the many migratory organisms
found intermittently in estuaries, sampling should occur during each season
of the year.
A major concern in estuarine systems is biological change due to pollution,
especially alterations to commercially important populations. The ratio of
annelids to mollusks and annelids to crustaceans has been used as an
indication of environmental stress. By comparing these ratios to the
Contamination Index (C.) and the Toxicity Index (T.), described in Appendix
A, area's highly contaminated by metals and organic chemicals can be
characterized (U.S. EPA, 1983^).
Briefly, contaminant factors (Cf) indicate the anthropogenic concentration
of individual contaminants, based on metal content and Si/Al ratios in
sediment. The Contamination Index (C.) is a sum of these contaminant
factors, giving equal weight to all m4tals, and thus has no ecological
significance until combined with biotoxicity data. The map of the
Chesapeake Bay in Figure 111-1 illustrates the degree of metal
contamination based on C.. The Toxicity Index (T.) is calculated using
contaminant factors and EPA "acute" criteria for The metals, i.e., the
concentration that may not be exceeded in a given environment at any time.
This index gives information pertinent to the toxicity of sediments to
aquatic life. Figure II1-2 illustrates the results of calculations of
Toxicity Indices for the Chesapeake Bay.
The Toxicity Index ranges from values of 1 to 20 where to lowest values
denote the least polluted conditions. Characteristies associated with
various values of T. may also be seen in Chapter IV, Table IY-3. The
Contamination Index is based on the calculation of the Quantity Cr (see
Appendix A) where Cf=0 when observed and predicted metal concentrations in
sediment are the same, Cf<0 when the observed is less than the predicted,
and C^>0 when the observea is greater than the predicted.
The juvenile index is often used to help predict future landings of certain
commercially important fish in estuaries. The juvenile index is simply the
number of first year fish of a species divided by the number of seine

Figure III-l. Degrees of metal contamination in the Chesapeake Bay based
on the Contamination Index (Cj). (from USEPA 1983c)

hauls. This index is then compared to juvenile indices from previous years
along with commercial fisheries landings data.
In summary, species diversity in estuaries is generally lower than in
adjacent freshwater or marine ecosystems. Either the changing environment
or the youth of estuaries or perhaps a combination of both is responsible
for this lack of species diversity. Indices of diversity that are used in
estuaries are the same as those employed in freshwater studies and have
been summarized in a previous document (U.S. EPA, 19831)).
Plankton include weak swimmers and drifting life forms. Most planktonic
organisms are small in size, and although they may be capable of localized
movement, their distribution is essentially governed by water movements.
Because of their unique salinity conditions and currents, individual
estuaries have characteristic plankton populations.
Three principal groups are included in the phytoplankton. They are
diatoms, dinoflagellajtes_ and nanop.lankton.	Like the ...phytoplankton- of-
freshwaters and oceans, estuarine phytoplankton require nutrients (such as
phosphorus, nitrogen, silicon), vitamins, iron, zinc and other trace metals
for growth. For photosynthesis to occur, adequate Tight must be available.
Suitable salinities must also be present for phytoplankton populations to
Nutrients generally are abundant in estuaries. Seasonal fluctuations in
nitrogen and phosphorus levels are often evident," and are related to
overland runoff and fertilizer application to agricultural lands. External
sources are not entirely responsible for nutrient levels in estuaries.
Cycling within estuaries also plays a role in plankton productivity. Thus
the turnover, or replenishment time (R), of nutrients is significant. in
determining their availability. Replenishment time is defined as R =
[S]/Sp, where [S] is the concentration of the nutrient in the phytoplankton
and Sp is the daily production rate measured in terms of particulate
content of that nutrient in the phytoplankton (Smayda 1983). Recycling
mechanisms may be separated into (1) excretion of remineralized nutrients
accompanying grazing by herbivorous zooplankton or benthic organisms, (2)
release through sediment roiling and diffusive flux of nutrients from the
interstitial water of sediments' following microbial remineralization, and
(3) kinetic, steady-state exchanges between nutrients present in the
particulate phase (phytoplankton, bacteria, sedimentary particles) and in
the dissolved phase. The importance of each of the preceding mechanisms is
dependent upon characteristics, viz. depth and vertical mixing, of specific
Although the phytoplankton of estuaries is an integral part of the eco-
system, its role is somewhat less important than in marine or freshwater
lake ecosystems. This is due partly to the large quantities of detritus
and bacteria that serve as an alternative food source for many primary
consumers. Estimates of primary production are generally calculated from

the utilization of nutrients (phosphates, C uptake, chlorophyll con-
centration) (Perkins 1974). The phytoplankton contribution to primary
productivity is often minimal in many coastal plain estuaries. Although
nutrients are abundant there, other factors limit phytoplankton production.
At the compensation depth, the amount of oxygen produced by photosynthesis
is equal to the amount utilized in respiration. Because of high tur-
bidity, the compensation depth in estuaries is relatively shallow thus
limiting the volume of water in which positive production occurs. Several
authors maintain the importance of phytoplankton in supporting estuarine
food webs, although the degree of contribution is- controversial. Boynton,
et al. (1982) provides a review of factors affecting phytoplankton pro-
duction by comparing numerous estuarine systems.
The flushing time of an estuary also affects the phytoplankton population.
Many estuaries have a relatively long flushing time and stable populations
are able to develop. The Columbia River estuary has a stable system with a
gradation from freshwater to brackish to marine plankton. In contrast, the
Margaree River (the Gulf of St. Lawrence) is drained completely at low
water and has no such gradation. Thus, high tide populations are typically
marine, while a freshwater population is evident at low tidei
The species composition of an estuary may be unique. Narragansett Bay for
example, is a shallow, well-mixed estuary located on the northeastern coast
of the United States. Surface salinity ranges from 20.5 ppt near river
mouths to 32.5 ppt at the mouth of the bay. Flushing time of the bay is
estimated at thirty days (Smayda 1983). Because of tidal and wind-induced
mixing, most of Narragansett Bay has neither a well-defined halocline or
thermocline. Seasonal variation of plankton is evident,1 although the
diatom Skeletonema costatum represents about 80% of total numerical
abundance over the annual cycle (Smayda 1983)'.. The major phytoplankton
bloom occurs during December, coinciding with the minimum incident
radiation and length of day. Blooms are regulated by temperature, light,
nutrients, grazing, hydrographic disturbances and possibly species inter-
actions. Neither blue-green algae nor dinoflagellates are important in
Narragansett Bay due to its relatively high salinity. Planktonic blue-
green algae tend to be more important in reduced salinities. Dino-
flagellates (viz. Prorocentrum triangulatum, Peridinium trochoideum,
Massartia rotundata, Olisthodiscus luteus"] occur sporadically during the
summer months, although diatoms continue to predominate. A succession of
diatom species occurs seasonally, although Skeletonema is prevalent during
all months. Detonula confervacea and Thalassiosi ra nordenskioeldii,
important secondary species during the winter-spring bloom, are replaced by
Leptocyl indrus danicus, L_. minimus, Cerataul ina pelagica, Asterionel 1 a
japonica, and Rhizosolenia fragi1issima.
Phytoplankton in the Naves ink River, New Jersey, were studied by Kawamura
(1966). Based on salinity, several zones with characteristic phytoplankton
were defined. Euglenoids dominated below 20 ppt. The zone in which
salinity lay between 20 and 22 ppt was populated by Rhizosolenia.
Cerataulina bergonii dominated in salinities ranging from 22 to 25 ppt.
Dinoflagellates, TTTcluding Peridinium conicoides-, P. trochoides, and
Glenodinium danicum, were prevalent in the outer regTon of the estuary.
Open water beyond the mouth of the estuary was populated mostly by
Skeletonema costatum. For regions with a fairly stable salinity gradient,
Kawamura (1966) noted the dominant forms as presented in Table' II1-1.

Salinity	Dominant Forms
2-5 ppt	Anabaenopsis sp., Microcystis sp.,
Synedra ulna, Melosira vanans.
9-10 ppt	Anabaena flos-aquae, Melosira varians,
Chaetoceros sp., Biddulphia spp.,
Coscinodfscus sp.
16 ppt	Euglenoids
20 ppt	Melosira varians, Chaetoceros debilis,
Ditylum brightwelli, Peridinians.
24-31 ppt	Skeletonema costatum, Rhizosolenia
longiseta, Biddulphia aurita,
Ditylum Srightwel1i, Dinophyceans.
from Kawamura (1966).
Zooplankton commonly found in estuarine reaches have been divided into the
following groups based upon their origins and salinity tolerances: (1)
Marine Coastal species, (2) Estuarine, arid (3) Freshwater. One of the
dominant copepods in estuaries is Acartia tonsa. Although it is not
utilized directly by humans, A. tonsa is a major food source for fish or
invertebrates that are consumed by humans (Jones and Stokes Assoc. 1981).
Several surveys of the zooplankton in Narragansett Bay have been conducted
and are summarized in Miller (1983). Copepods were the dominant group,
comprising 80% or more of the individuals on an annual average. Important
species were Acartia clausi, /\. tonsa, Pseudocalanus minutus and Oithona
spp. Rotifers were abundant in late winter, and cladocerans were abundant
in early summer. Flushing reaches a peak in March-April, coinciding with a
low in biomass.
Zooplankton have also been studied extensively in the Chesapeake and
Delaware Bays, resulting in the following list of predominant species:
(1) Coastal:
copepods - Centropages typicus, C. hamatus, Labidocera aestiva,
Temora longicorms, Paracalanus parvus, Pseudo-
cal anus minutus;
cladocerans - Penilia avirostris, Evadne nordmanni.
(2) Estuarine:
copepods - Acartia tonsa, Acartia clausi, Eurytemora affinis,
Scottolana canadensis (harpacticoid), and PseuUcH
diaptomus coronatus;

cladocerans - Podon polyphemoides.
(3) Freshwater:
copepods - Cyclops viridis;
cladocerans - Bosmina longirostris.
Grazing by zooplankton is an important factor in trtfc confcro;!' off to-
pi ank ton populations, although the precise role pla/ei % not yetf. well-
defined. The population dynamics of zooplanktor o/in tfie ea-'Si;' citast,
including seasonal cycles and predation by cteroffvvarres;,. i11 beetT o&served iiin
Yaquina Bay, Oregon, and it is probable that	preriartors'. Hiiit
zooplankton densities.
Comparatively less information is available on Gul^ caas.fr zllamnlklto:n
distributions than for the Atlantic coast. Some refereneas far zooptflaisifctaiiirt
community structure and distributions in Louisiana estuaries arrd^ cassstail
waters are: Brice, 1983; Binford, 1975; Cuzon du Rss.t* 19.63;. DnajmrncnwH,
1976; Gillespie, 1971.
Planktonic larval forms of organisms such as oysters and: crabs are" imcTiiista!
in the temporary zooplankton. The veliger larvae oS imxl1'uscs freozmie part
of the plankton during the spring and summer. Some esfrjarrnfc wo,mrx also
have planktonic larval forms. The occurrence of the92 fgrmsr i-sr-. gpvarmesdH toy
the breeding season of the adults. Environmental toT-erufreas- crfi the Haunral
forms of the blue crab (Cal 1 inectes sapidus) and tlTe Aflrericam ouster
(Crassostrea virginica) are found in Appendix B (e,f)..
To persist in an estuary, 'zooplankton, like phytopiaiktorr, must hravz* rates
of population increase at least equal to the rates asff 'less- dUe: tiro tfcilail
flushing and river flow. High flushing rates gejeralTy, p.iroJiiiifc*'t tfae
development of an endemic plankton population, an& qTianktorr fmsnd
merely resemble those found in the ocean offshore. Stadias- of gogiiili-Bttfiajin
budgets have been made on a few estuaries. (NarraganseSA 3fcy., Great. fftod,
Moriches Bay) and are mentioned briefly by Miller (19S3;)V
The following articles contain information on metttadis'. i,m z.ooj?jT!aim!ktffl;ni
research: Computer and electronic processing of zcjEaplianfcSanj CJMiFiries
1980); Gear used (Schindler 1969, Josai 1970); SamtyHmg; for biiiomvass-
standing stock (Ahlstrom et al . 1969, Colebrook 1S3>, TV?ra
macro- and microbenthos are respectively larger and smaller than meio-
benthos (Wolff 1983).
Although the diversity of the benthos in estuaries is low compared to other
ecosystems, benthic production is relatively high. A high level of food
(detritus and plankton) and shallow depths contribute to the.
characteristically high benthic production noted in estuaries. Detritus is
readily available to the benthos because it sinks through the shallow
water. In addition, waves and tidal currents promote resuspension of
particles, making them available to filter-feeders. The predominance of
relatively opportunistic species, with one or more generations per year,
results in a high turnover of biomass and thus high production. Macrofauna
have high biomass and low turnover times and hence have economic and
commercial value. Meiofauna, with low biomass and high turnover rate, play
an essential role as nutrient regenerators and food for higher trophic
levels (Tenore et al. 1977, Mclntyre and Murison 1973, Ajheit and Scheibel
Infaunal Forms
The benthos comprises invertebrates such as thre-ad worms, bristle worms,
ostracods, and copepods as well as commercially important species of
crustaceans and molluscs. Nematodes (Nematoda, thread worms) dominate the
shallow water meiofauna of estuarine sediments. In addition to nematodes,
permanent meiofauna include copepods, gastrotrichs, oligochaetes, rotifers
and turbellarians. Juvenile macrofauna comprise the temporary meiofauna.
Generally, coarser sediments support a greater diversity of species than
finer estuarine sediments (Ferris and Ferris 1979).. Polychaetes
(Polychaeta:Annelida, bristle worms) are abundant in the soft bottom,
especially within the sediment of intertidal mud flats.
Studies have used polychaete populations to characterize water bodies as
having healthy, polluted, or very polluted bottoms. The use of benthic
organisms as indicator species is well-documented for freshwater studies
whereas studies in the estuarine/marine environment are relatively few
(Reish 1979). Although the species composition in freshwater is different
than marine species composition, the concept of using benthic communities
as indicators of pollution remains the same. In estuarine systems,
polychaete species composition changes from zones characterized as healthy
to those classified as polluted. As shown in Table III-2, there is a
concurrent decrease in dissolved oxygen concentration, an increase in the
organic carbon content of the soil, and a reduction in the number of
organisms until all species are absent (Reish 1979). However, the validity
of using polychaetes as indicator species has been questioned, since
polychaetes such as Capitella capitata,' an opportunistic organism whose
presence has often been cited as an indication of pollution, also occur in
pristine estuarine areas (Reish 1979). The following literature con-
tributions also pertain to the use of benthos as indicators of pollution:
Sediment bacteria as indicators (Erkenbrecher 1980); Meiofauna as indi-
cators (Coull et al 1981, Raffaelli 1981, Warwick 1981); Macrofauna as
indicators (Gray and Mirza 1979).


Healthy bottom.
Semitic allli)

/httrx I purvux.
hollOlll 1. I'ttfxtltHO
htiiitiiii II,
Very polluted

CoUUfJf 1 (I'lt/li/ll.
/mm ibrwu hnnu.
( itptlfllll
< hjracicriMic
Nrrrts pro* rm
Ihiriitifn tutu utiihi
t Uplhitil
no jnim.iK
Numhei of dnmul

20 (l depih

Crustaceans include microorganisms such as ostracods,..copepods and isopods
along with commercially important macroorganisms such as crabs, shrimp and
lobsters. The crabs (Arthropoda:Crustacea:Decapoda:Brachyura) that have
successfully colonized North American estuarine systems are listed in Table
111-3. Brachyuran crabs have a complex ontogeny. They are released from
the female as zoeae, or free swimming larvae, into meso- to euhaline
waters. The zoeae undergo a series of molts before reaching the megalopa
stage. The megalopa metamorphoses into the first crab stage, which becomes
the adult following successive molts (Williams and Duke 1983). It has been
noted that above and below the preferred temperature range, the length of
time required for larval development increases. Two species of Cancer that
have commerical value, C^ magister (Pacific Dungeness crab! and C.
irroratus (Rock crab), normally enter estuaries only in high salinity
regions. Larvae of C. magi ster and C. irroratus prefer conditions of 25-30
ppt, 10-13C and 23.1^32.3 ppt, 13-2TC, respectively.
Callinectes sapidus, the blue crab, supports a major fishery in the United
States. Tfie species lives in fresh water to salinities as high as 117 ppt
(large males have been recorded in salt springs over 180 miles from the sea
in Marion County, Florida) and from the water's edge to 35 meter depths.
Appendix B (Table le) contains information pertaining to the life cycle of
the blue crab. Additional information on general life histories of crabs
and other commercially important shellfish in Gulf Coast waters is compiled
by Benson (1982). The family Portunidae is also represented by Carcinus
maenas in estuaries. The green or shore crab normally inhabits waters
ranging in salinity from 10-33 ppt, and depths of less than 5-6 m (Williams
and Duke 1979). Other crabs commonly found in North American estuaries are
listed in Table 111-3. Among the xanthid crabs, only Menippe mercenaria,
the stone crab, has any fishery value. The major commercial fishery for
stone crabs occurs in Florida, where its flesh is considered a delicacy.
Most of the information about shrimp pertains to the commercially valuable
penaeid shrimp, Penaeus duorarum (pink shrimp), Penaeus aztecus (brown
shrimp) and Penaeus setiferus (white shrimp). Penaeid shrimp are dependent
upon estuaries during their transformation from the postlarval stage to the
juvenile stage. Adults migrate from the estuarine environment to coastal
and nearshore oceanic waters (Couch 1979). The life cycle of the penaeid
shrimp is illustrated in Figure 111-3. The range of the brown shrimp
extends from Martha's Vineyard, Massachusetts, through the Gulf of Mexico
to the Yucatan Peninsula, Mexico (Turner, 1983). Brown shrimp spawn in
offshore marine waters deeper than 18 m (59 ft). Movement of postlarvae
into estuaries has been observed from January through June in Louisiana. A
peak migration from March to April was noted for Galveston Bay, Texas.
Postlarval brown shrimp prefer salinities of 10 to 20 ppt, and temperatures
above 15C. Transformation from postlarvae to juveniles occurs four to six
weeks after entering the estuary. Juveniles remain in shallow estuarine
areas (near the marsh-water or mangrove-water interface or in seagrass
beds) that provide feeding habitat and protection from predators until they
reach 60 to 70 mm (2.4 to 2.8 inches) total length (TL). They move into
deeper, open water,, and begin gulfward migration when they reach 90 to 110
mm (3.5 to 4.3 inches) (Turner and Brody, 1983).

Infnoider Brachyura
Section Cancndea
Family Cancndae
Cancer irroratus Say. Rock crab
Cancer magister Dana. Dungenesscrab
Section Brachyrtiyncha
Superfamily Portunoidea
Family Portumdae, "Swimming" cribs
Subfamily Portuninae
CaJlinectes sapidus Rath burn. Blue
Carcimu maenas (Linnaeus). Green
or shore crab
Superfamily Xinthoidea
Family Xanthidae
Subfamily Xanthinae. "Mud" crabs
Catalepiodius (=Ltptodtus)
flortdanus (Gibbes)
Eurvpanopeus dtpressui
(S. I. Smith)
Neopanope savi (S. I. Smith)*
Panopeusherbstu A. Milne Edwards
Rhthropanoptus hamsit (Gould)
Subfamily Menippinae
Mtnippe mercertaria (Say). Stone
Family Grapsidae
Subfamily Vammnae
Hemtgrapsus nudus (Dana), Purple
shore crab*
Subfamily Sesarrmnae
Sesarma cinertum (Bosc), Wharf
Sesarma rtnculanim (Say). "Mareh
Superfamily Ocypodoidea
Family Ocypodidae
Subfamily Ocypodinae
Uca minor (Le Conte). Red jointed
Uca pugilaior (Bosc), Sand fiddler
Uca pugnax (Smith). Mud fiddler
T ropical-polyhaline
Tem pe rate-tropic aJ - mesohaline
Temperate -oligo-rnesohalwe
Warm lemperaie-sutxropical-mesopolyhaline
Tempe rate-polyhaline-Semite rrcsinaJ
Temperate -oligo-mesohaline-semiterrestnaJ
Temperate-subtropical-me sopolyhaline-
Temperate-meso polyhaline - semitencstnal
'Species inumaicly associated with communities reported here and pollution studies published
(from Williams and Duke 1979)


Figure 111-3. Life Cycle of the Penaeid Shrimp, (from Couch 1979)
Postlarval white shrimp migrate into estuaries from late spring to early
fall, and are most abundant 1n Louisiana estuaries from June through
September. They, are generally found in lower salinity waters than brown
shrimp and prefer water temperatures higher than 15C. White shrimp (120
to 140 mn) leave Gulf of Mexico embayments from September to December, as
the water cools.
Finally, the grass shrimp (Paleomonetes sp.) of estuaries commonly live in
patches of grasses growing in shallow water. Because of aquarium suita-
bility, members of palaemonidae are often used in pollution studies.
Moll uses
The last major group in the estuarine benthos is the molluscs. The
molluscs include clams, mussels, scallops, oysters and snails. Clams of
major importance include Mya arenaria (soft shell clam), Mercenaria
mercenaria (hard shell clam), and Rangfa~cuneata (brackish water clam).

The soft shell clam is common in bays and estuaries on both the east and
west coasts of the United States, although it is commercially important
only on the east coast. Soft shell clams can tolerate a wide range of
salinities and temperatures. Larval development occurs at salinities from
16-32 ppt, and at temperatures of 17-23C. Mya arenaria occurs in a
variety of substrates, but prefers a mixture of sand and mud (Jones and
Stokes Assoc. 1981). Hard clams (Mercenaria mercenaria) can tolerate high
pollution and low oxygen levels; thus, they thrive where other species
cannot compete. Hard clams prefer substrates of sand or sandy clay
(Beccasio et al. 1980). The littleneck clam (Protothaca staminea) is a
hardshell species found in estuaries, bays and open coastlines along the
Pacific coast. It ranges from the Aleutian Islands to Socorro Island,
Mexico. Minimum salinity for survival is 20.0 ppt (Rodnick and Li 1983).
The brackish water clam is found in low salinity bays and estuaries from
the Chesapeake Bay to Mexico (Haven 1978). Rangia cuneata can survive in
fresh water, but needs brackish water for spawning (Menzel 1979).
The bay mussel (Mytil us edul is) is found worldwide in estuaries and bays.
It is tolerant of variations in temperature, salinity and dissolved oxygen.
Although the bay mussel is under stress at salinities less than 14-16 ppt,
it can survive at 4 ppt for short periods of time. This mussel attaches to
any hard substrate and may be found on rocks, stones, shingles, dead
shells, ship bottoms, piers, harbor walls and compacted mud and sand (Jones
and Stokes Assoc. 1981).
Bay scallops (Argopectin irradians) are usually found in shallow estuarine
eelgrass beds, but may occur in depths to 18 m (Beccasio et al. 1980).
They ingest detritus, bacteria and phytoplankton. The large amount of
detritus consumed reflects its great availability in estuarine systems
(McLusky 1981).
The American oyster (Crassostrea virginica) is a permanent resident or
estuaries. It is a valuable component ofeast coast fisheries. Oysters
prefer salinities between 14.1 ppt and 22.2 ppt, although they are able to
tolerate a wider range, from 4-5 ppt to 35 ppt (Castagna and Chanley 1973).
Within the range of distribution of virginica, the species lives in
water temperatures from about 1C (during the winter in northern states) to
about 36C (in Texas, Florida, and Louisiana) (Galtsoff 1964). Larvae
develop well in depths from 2 to 8 meters at temperatures of 17.5 to
32.2C. The oyster population in high salinities is limited by oyster
drills (e.g. gastropod Urosalpinx cinerea) and parasites (MSX and
Dermocystidium) (Haven 1978). Spawning by oysters is dependent upon
temperature, and commences when the water reaches from 16-28C depending
upon geographic area (Bardach et al. 1972, Ingle 1951). After 6-14 days,
the eggs hatch and the free-swimming larvae settle on a suitable hard
substrate. Oysters filter food from the water column and deposit organic
material (feces and pseudofeces) which is then available to other benthic
organisms; thus, they play a valuable role in increasing the productivity
of the area in which they live (McLusky 1981).
Temperature tolerances of American oysters differ with latitude. Oysters
at latitudes north of Cape Hatteras can survive at temperatures less than
0C for 4 to 6 weeks, while Gulf of Mexico oysters die if subjected to such
low temperatures (Cake 1983). Temperatures required for mass spawning also

differ with latitude. Apalachicola Bay reached temperatures of 26-28C
before mass spawning occurred, while a low of 16.4C induced mass spawning
in Long Island Sound, New York (Ingle 1951). Other oyster species commonly
found in estuaries of the United States are Crassostrea gigas (Pacific
oyster) and Ostrea edulis (flat oyster).
Snails (Gastropoda) have not been studied as extensively as the molluscs
discussed above. In general, adult snails are slow moving, benthic, and
able- to endure a variety of temperatures and salinities. After the eggs
are hatched, most snails have a planktonic stage; a few emerge as crawling
juveniles. Many snails are vegetarians and scrape algae from surfaces.
Some carnivorous snails use their radulas to drill holes in other shelled
animals (e.g., oyster drills). Other snails consume gastropods whole,
digesting the tissue and regurgitating the empty shells (Menzel 1979).
More information about the distributions and habitats of NE Gulf gastropods
is described in Heard (1982).
References on methodc1cgy for the study of estuarine microbiota and benthos
include: Holme and Mclntyre 1971, Hulings and Gray 1971, U.S. EPA 1978,
Uhlig et al. 1973, de Jonge and Bouman 1977, Federle and White 1982, White
et al. 1979, Montagna 1982.
In conclusion, the estuarine benthos play an important role in estuarine
ecosystems. The nematodes and polychaetes, along with the commercially
important shellfishes, contribute to the high productivity noted in most
estuaries. The benthos are generally able to tolerate variations in
temperature and salinity. Thus, they are able to live, and often thrive,
in estuaries.
Submerged aquatic vegetation (SAV) plays an important role in the estuarine
ecosystem, providing habitat, substrate stability and nourishment. These
functions are the subject of discussion in this section. However, sub-
merged aquatic vegetation also provides a valuable frame of reference
against which to assess the health of an estuary, or portion of an estuary.
The importance of SAV to an analysis of the uses of an estuarine waterbody
will be discussed further in Chapter IV, Interpretation.
Role of SAV in the Estuary
Plants increase the stability of bottom sediments and reduce shoreline
erosion. In addition, because the plants help to slow the tidal current,
more materials may settle from suspension, augmenting the substrate and
decreasing turbidity. Species differ in their ability to reduce turbidity.
For example, areas dominated by Potamogeton perfoliatus (a highly branched
species) were more instrumental in improving water clarity than areas where
Potamogeton pectinatus (a thin-bladed single leaf species) dominated
(Boynton et al. 1981).
Aquatic plants serve as both sources and sinks for nutrients. During the
growing season, SAV absorbs nutrients from the water and sediments.
Release of nutrients occurs when the vegetation dies. Submerged aquatic-
vegetation also provides valuable habitat for fish and crabs, along with

molluscs and other epifauna. SAV provides shelter, spawning areas and
shade for fish, while roots, stems and leaves provide firm bases for the
attachment of mussels, barnacles, molluscs and other epifauna. Thus,
vegetated bottoms exhibit a greater species richness than unvegetated
bottoms (U.S. EPA 1982).
Stevenson and Confer (1978) cited a study (Baker 1918) which emphasized the
large number of organisms associated with submerged aquatic vegetation.
Over a 450 sq. mile area, Potamogeton sp. harbored 247,500 molluscs and
90,000 associated animals (total fauna, 337,500) and Myriophyllum sp.
harbored 45,000 molluscs with 56,250 associated animal's (total Fauna,
101,250). Epiphytes and macroalgae constitute a significant and sometimes
a dominant feature of SAV community production and biomass, as can be seen
from Table III-4. Fish such as silversides (Menidia menidia), fourspine
stickleback (Ape!tes quadracus) and pipefish (Syngnathus fuscus) take
advantage of this abundant epifauna for food.
Eel grass beds also provide protection for amphipods from predatory finfish.
Grass shrimp (Palaeomonetes pugio) seek protection from predatory killifish
(Fundulus heteroclitus) TF eel grass beds. Young and molting crabs find
shelter in areas of submerged aquatic vegetation as well.
Aquatic vegetation enters the food chain though grazing by waterfowl or as
detritus passing through epifaunal and infaunal invertebrates to small and
large fish. The extent to which SAV is used as a food source is determined
mainly by two methods. The first is direct visual identification of mate-
rial in an organism's digestive system. Such analyses are time-consuming,
and the degree to which food items can be identified is often limited to
largec 1 tarns that are resistant to digestion. The second techique is based
on C :C ratios 1n plants and associated predators. This method assumes
that animals feeding on a particular plant will, in time, reflect the food
source ratio. Problems arise wherk aryunals feed on a variety of species," or
if several plants have similar C :C ratios. In addition, determination
of C :C ratios 1s a relatively expensive procedure.
Submerged aquatic vegetation also plays a role in nutrient cycling in
estuaries. Since plants act as nutrient traps and sinks for dissolved
minerals, SAV communities are capable of removing nutrients from the water
column and incorporating them into biomass. Iron and calcium were found to
be absorbed from the sediment by Myriophyllum spicatum. The release of
nutrients and minerals occurs by excretion by living plants or by the death
and decomposition of SAV.
Distribution of SAV
The distribution of SAV species is determined largely by salinity. The
degree of flooding also affects vegetation distribution and is particularly
important for Gulf Coast estuaries (Sasser 1977). In a study of the
Chesapeake Bay, Steenis (1970, cited by Stevenson andConfer 1978) noted
the following tolerance levels for Bay vegetation:

a. Location Species
Seagrass Epiphytes Benthic micro-algae Macro-algae Phytoplankton Reference
N.Carolina Zostera
Ches. Bay
Zostera*1	0.48
P.pectinatus 0.5-2.2
P.perfoliatus 1-3.0
Daily estimates In summer period.
		Jones 1968
		Marshall 1970
91	Wetzel 1964
Penhale 1977
0.09	Murray (pers.comm.
0.3-1.0	Kaumeyer et al. 19
0.5-1.0	Kaumeyer et al. 19
b. Location Species
Seagrass Epiphytes Benthic micro-algae Macro-algae Phytoplankton Reference
N.Carolina Zostera
Ches. Bay
Gessner and Hammer
McRoy 1970
Penhale 1977
Staver et al. 1981
Staver et al. 1981
(from USEPA 1982)

3 ppt
Najas guadalupensis (southern naiad)
3-5 ppt
Chara spp. (muskgrass)
Vallisneria americana (wildcelery)
12-13 ppt
El odea canadensis (elodea)
Myriophyllum spicatum (Eurasian waterailfoi1)
Ceratophyllum demersum (coontail)
20-25 ppt
Potamogeton perfoliatus (redhead grass)
Potamogeton pectinatus (sago pondweed)
Zannichellia palustris (horned pondweed)
over 30 ppt
Ruppia maritima (widgeongrass)
Zostera marina (eelgrass)
The depth at which vegetation is able to survive is directly related to the
penetration of incident radiation. Plants need light for photosynthesis,
therefore turbidity affects their distribution by decreasing the amount of
sunlight reaching greater depths. Temperature also affects the distribu-
tion of SAY, and exerts considerable influence upon, its vegetative growth
and flowering. These factors are constdered in more detail' in Appendix C
for several east-coast species.
Three associations of submerged aquatic vegetation were described for the
Chesapeake Bay, based on their co-occurrence in mixed beds. The first
association tolerates fresh to slightly brackish water (upper reaches of
the Bay) and includes bushy pondweed, coontail, elodea (waterweed), and
wildcelery. The middle reaches of the Bay have associations of widgeon-
grass, Eurasian watenrii 1 foil, sago pondweed, redhead grass, horned
pondweed, and wildcelery. Finally, in the lower reaches of the Bay,
eel grass and widgeongrass predominate. The kinds of submerged aquatic
vegetation encountered in the Chesapeake Bay from 1971 to 1981 are listed
in Table 111-5.
The major species of SAV found on the eastern coast of the United States
(their distribution, environmental tolerances and consumer utilization) are
listed in Appendix C. The species that are especially important as food
items for waterfowl are coontail, muskgrass, bushy pondweed, sago pondweed,
redhead grass, widgeongrass and wildcelery. Grazing by waterfowl is a
primary force in the management of aquatic vegetation. Some aquatic
vegetation, although it provides protective cover for wildlife, is con-
sidered a nuisance because of excessive growth and clogging of waterways.
Elodea, Eurasian watermilfoi1, and sago pondweed are among those considered
to be pest species.
Information concerning aquatic vegetation in southern U.S. estuaries is
found in literature by Chabreck and Condrey 1979, Beal 1977, and Correll
and Correll 1972.

Vascular	Macro-
Species	Plants^	Algae1
1.	Redhead grass (Potamogeton perfollatus)	X
2.	Widgeongrass (Ruppia maritima)	X
3.	Eurasian watermilfoil (Myrlophyllum spicatum)	X
4.	Eelgrass (Zostera marina)	X
5 .	Sago pondweed (Pj^ pectinatus) X
6.	Horned-pondweed (Zanlchellla palu3trl9)	X
7.	Wildcelery (Vallisneria americana)	X
8.	Common elodea (Elodea canadensis)	X
9.	Naiad (Najas guadalupensla)	X
10.	Muskgrass (Chara spp.)	X
11.	Slender pondweed (j?. puslllus)	X
12.	Coontail (Ceratophyllum demersum)	X
13.	Unidentified fragments	X
14.	Curly pondweed (Potamogeton crispus)	X
15.	Sea lettuce (Ulva spp.)	X
16.	Agardhiella spp.	X
17.	Unidentified filamentous green algae	X
18.	Unidentified green algae	X
19.	Gracilaria spp.	X
20.	Water-stargra8S (Heteranthera dubia)	X
21.	Unidentified alga	X
22.	Enteromorpha spp.	X
23.	Ceramium	X
24.	Polysiphonia	X
25.	Dasya spp.	X
26.	Unidentified red alga	X
27.	Unidentified brown alga	X
28.	Champia parvula	X
1 An "X" in the column indicates the type of SAV.
(from USEPA 1982)

Adverse Impacts on SAV
Portions of the estuary may become enriched beyond their flushing and
assimilative capacity and elevated levels of nitrogen and phosphorus begin
to support abnormal algal growth and eutrophic conditions. Algal growths
are important because they act to diminish to penetration of sunlight into
the water. Submerged aquatic vegetation is dependent upon sunlight for
photosynthesis, and when light penetration is diminished too much by algal
growths, the SAV will be affected. These factors are discussed in detail
in Chapter II.
Runoff may also introduce herbicides to the estuarine ecosystem. The
magnitude of detrimental effects depends upon the particular herbicide,
and its persistence in the environment and potential for leaching.
Furthermore, several herbicides have a synergistic effect along with
nutrients, its potential for leaching and persistence in the environment.
Several pathogens may attack and diminish the size of submerged aquatic
vegetation beds. Rhizoctonia solani is a fungus that attacks the majority
of duck food pi ants, but i s especially pathogenic to sago pondweed
(Stevenson and Confer 1978). Lake Venice Disease causes a gradual wasting
away of the host pi-ant; it is manifested as a brownish, silt-like coating
on leaves and stems. Milfoil is attacked by the Northeast Disease, which
gradually causes the leaves to break off, leaving a blackened stem.
Survey Techniques
Aerial, surface and subsurface methods are used to prepare maps delineating
vegetation types and percent cover. Plant growth stage (e.g. season) is
critical when planning a plant survey. For example,- early summer is the
optimum time of year to record maximum plant coverage in the Chesapeake Bay
but a different time of year may be more appropriate -in other parts of the
Country. Water transparency is also important to show plant growth.
Aerial methods are useful in determining the distribution of plant assoc-
iations, irregular features, normal seasonal changes and perturbations
caused by pollutants. Mapping cameras are designed to photograph large
areas without distortion. Areas of SAV beds may be derived from topo-
graphic quadrangles (Raschke 1983). The Earth Resources Observation System
(EROS) Data Center may be used to obtain listings and photographs already
available for a particular area.
Surface or ground maps can be prepared if the area is relatively small.
Distances can be determined by ruled tapes, graduated lines, range finders,
or, if more accuracy is required, surveyor's tools. Field observations of
species may be supplemented by photographs. Divers can mark subsurface
beds with bouys to facilitate determination of bed shapes and areas from
the surface.
Regional surveys of flora give qualitative information, based upon visual
observation and collection of plant types. To obtain more quantitative
information, line transects, belt transects, or quadrats may be employed
(Raschke 1983). Use of line transects involves placement of a weighted
nylon or lead cord along a compass line and recording plant species and
linear distance occupied. A belt transect can be treated as a series of
quadrats,, with each quadrat defined as the region photographed from a

standard height or a marked area. The technique of sampling within a
quadrat or plot of standard size is applicable to shallow and deep water.
Where visibility is poor, epibenthic samplers can be used.
A fundamental characteristic of the community structure of submerged
aquatic vegetation is the leaf area index (LAI). It is defined as the
amount of photosynthetic surface per unit of biomass (U.S. EPA 1982). The
photosynthetic area is measured by obtaining a two-dimensional outline of
the frond, and determining the area with a planimeter. Leaf area index
differences demonstrate the importance of light in regulating SAV
communities and their adaptability to different light regimes. The
greatest LAI values occur for mixed beds of Zostera and Ruppia; lower
values were found for pure stands of Zostera and Ruppia"(U.S. EPA 1982).
The information presented here 1s a brief overview of survey techniques
used in the sampling of SAV. Supplementary discussions are found in
literature by Kadlec and Wentz (1974), and Down (1983).
Systems of Classification
Various authors have attempted to devise systems to classify estuarine
organisms. Because salinity is the most dominant physical factor affecting
the distribution of organisms, it is often used as the basis for classi-
fication systems. McLusky (1971, 1981) divides estuarine organisms into
the following categories:
1.	Oligohaline organisms - The majority of animals" living in rivers
and other fresh waters do not tolerate salinities greater than 0.1
ppt but some, the oligohaline species, persist at salinities up to
5 ppt.
2.	True estuarine organisms - These are mostly animals with marine
affinities which live in the central parts of estuaries. Most of
them are capable of living in the sea but are not found there,
apparently because of competition from other animals.
3.	Euryhaline marine organisms - These constitute the majority of
organisms living in estuaries with their distribution ranging from
the sea into the central part of estuaries. Many	disappear by
18 ppt but a few survive at salinities down to 5 ppt.
4.	Stenohaline marine organisms - These 'occur in the mouths of
estuaries at salinities down to 25 ppt.
5.	Migrants - These animals, mostly fish and crabs, spend only a part
of their life in estuaries with some, such as flounder
(Platichthys) feeding in estuaries, and others, such as salmon
(Salmo salar) or eels (Anguilla anguilla) using estuaries as routes
to and from rivers and the sea.

A similar scheme of classification, shown in Table 111-6, was defined by
Remane. Components of fauna are separated according to the sources from
which they arrived at their present-day habitat, e.g., from the sea, from
freshwater and from the land. Marine and freshwater components are further
divided based on salinity tolerances. The terrestrial component may be
subdivided into those species which escape the effects of immersion by
moving upwards when the tide floods the upper shore, and those species
which remain on the shore and are able to survive submersion for several
Day (1951, cited by Haedrich 1983) divided estuarine fishes into five
categories: freshwater fishes found near the head of the estuary,
stenohallne marine forms from the seaward end of the estuary, euryhaline
marine forms occurring over wide areas, the truly estuarine fishes found
only in the estuary, and migratory forms that either pass through the
estuary or enter it only occasionally. A modified version of this
classification was presented by McHugh (1967). His categories were:
1.	Freshwater fish species that occasionally enter brackish waters.
2.	Truly estuarine species which spend their entire lives in the
3.	Anadromous and catadromous species.
4.	Marine- species which pay regular seasonal visits to the estuary,
usually as adults.
5.	Marine species which use the estuary primarily as a nursery ground,
usually spawning and spending much of their adult life at sea, but
often returning seasonally to the estuary.
6.	Adventitious visitors which appear irregularly and have no apparent
estuarine requirements.
Day's classification of biota and the Venice System of dividing estuaries
into six salinity ranges were combined by Carriker (1967) to develop Table
III-7. The right half of the table shows the biotic categories and the
approximate penetration of animals relative to salinity zones in the
Salinity Preferences
Some freshwater fish species may occasionally stray into brackish waters.
White catfish (Ictalurus catus) is a salt-tolerant freshwater form found in
estuaries along the east coast of the United States. Three other species
that are primarily freshwater, but have been captured in higher salinity
areas are longnose gar (Lepisosteus osseus), bluegill (Lepomis macrochirus)
and the flier (Centrarchus macropterus) (McHugh 1967).
Very few fish are considered to be truly estuarine. McHugh (1967). mentions
only two species that he Considers endemic to the estuarine environment.
They are the striped killifish (Fundulus majalis) and the skilletfish

The stenohaline marine component, not penetrating below 30 ppt
The euryhaline marine component
First grade, penetrate to 15 ppt
Second grade, penetrate to 8 ppt
Third grade, penetrate to 3 ppt
Fourth grade, penetrate to below 3 ppt
Brackish water component, lives in estuaries, but not in sea
The stenohaline freshwater component, not penetrating above 0.5 ppt
The euryhaline freshwater component
First grade, penetrate to 3 ppt
Second grade, penetrate to 8 ppt
Third grade, penetrate, above 8_.ppt __
Brackish water component, lives in estuaries, but not in freshwater
III.	MIGRATORY COMPONENT migrates through estuaries from sea to freshwater
or vice versa
Anadromous, ascending rivers to spawn
Catadromous, descending to the sea to spawn
Tolerant of Submersion
Intolerant of Submersion
(from Green 1967)

Venice System
Sal Inity
\ O/OO Zones
Ecological Classification
Types of Organises and Approximate Range of Distribution In
	Estuary, Relative to Division and Salinities	
Upper Reaches
Middle Reaches
O.S	Limnetic
O.S-5	OUgohallne
5-18	Hesohallne Mixohallne
18-25	Polyhallne
01 IgohalIne
Lower Reaches
Euryhaline Migrants
(from Carriker 1967)
(Gobiesox strumosus). The fourspine stickleback (Apeltes quadracus) is a
small fish that is abundant in estuaries but cannot be considered truly
estuarine because it enters freshwater occasionally. Beccasio et al. (1980)
included killifish, silverside, anchovy and hogchoker in the category of
truly estuarine species. Other authors concede the existence of truly
estuarine species although they fail to mention them as such. Instead,
fish are categorized as spending a major portion 'of their life cycle in an
estuary, as being dependent on the estuary at some time, or as being the
dominant species present.
A listing of species commonly found in North American Atlantic/Gulf coast
estuaries and their salinity tolerances/preferences as adults is contained
1n Table 111-8. It should be noted, however, that salinity preferences of
some fish may change at the time of migration. For example, adult stickle-
back (Gasterosteus aculeatus) prefer freshwater in March and saltwater in
June/July (McLusky 1971). Salinity tolerances also differ depending on the
organism's stage of life. Salinity tolerances or requirements of juveniles
may be unlike those of the adult.
The Gulf of Mexico estuaries support populations of fish that are also
found along the Atlantic coast. For example, spot (Leiostomus xanthurus)
are abundant along the Gulf and the Atlantic coast.s. The Atlantic croaker
ranges from the New England States to South America, although it is
basically a southern species Important 1n the Gulf of Mexico and South
Atlantic Bight. Gulf menhaden is an estuarine dependent species that
primarily Inhabits northern Gulf of Mexico waters. Southern kingfish
(Menticirrhus americanus) have been collected along the coasts from Long

Scientific Name
Alosa spp.
Brevoorti a patronus
Brevoortfa tyrannus
Cynoscion~ regali s
Ictalurus catus
Ictalurus punctatus
Leiostomus xanthurus
Mem" di a meni di a
Micropogonias undulatus
Mo rone amencana
Morone saxatilis
Perca flavescens
Pomatomus saltatrix
Common Name
Herring, shad, alewife
Gulf menhaden
Atlantic menhaden
Weakfi sh
White catfish
Channel catfish
Atlantic silverside
Atlantic croaker
White perch
Striped bass
Yellow Perch
B1uefi sh
Salinity (ppt)
(from U.S. EPA, 1983a)
Island Sound, New York, to Port Isabel, Texas (Sikora and Sikora 1982).
They are estuarine dependent, and larval southern kingfish move from
offshore spawning areas to estuarine nursery areas. Salinity preferences-
of southern kingfish varies with size. Only the smaller juveniles are
found in waters with salinities of less than 10 ppt. Larger juveniles
(>150 mm or 5.9 inches standard length, SL) are rarely taken in waters with
salinities less than 20 ppt, and are usually found in deeper waters such as
sounds, near the mouths of passes, or near barrier islands (Sikora and
Sikora 1982). The most common fish found in Gulf of Mexico estuaries are
listed in Table III-9, along with the range of salinities in which they
were captured (Perret et al. 1971). Additional information on the envi-
ronmental requirements of Gulf coast species is presented in Appendix D.
Appendix B contains a listing of habitat requirements of major Atlantic
coast estuarine species during their life cycles. More detailed descrip-
tions of habitat requirements of egg, larval and juvenile stages of fishes
of the Mid-Atlantic bight are contained in several publications by the
United States Fish and Wildlife service (1978, Volumes I-VI). Mansueti and
Hardy (1967) also published information regarding fishes of the Chesapeake
Bay region. These-reports contain illustrations of the life stages for
many species, alo.ng with pertinent information regarding preferred sub-
strate, salinity and temperature. Although the books focus on egg, larval,
and juvenile stages, the adult stage is also addressed.
Annual Cycles of Fish in Estuaries
Annual cycles and abundances of species are important in the ecology of
estuaries. The composition of the estuarine fauna varies seasonally,
reflecting the life histories of species. Anadromous fishes pass through

Salinity (ppt)
range where
 range at number of
collection individuals
Scientific Name	Common Name	sites / captured
Anchoa hepsetus
Striped anchovy
Anchoa mitchilli
Bay anchovy
Arius felis
Sea catfish
Bagre marinus
Gafftopsail catfish
Brevoortia patronus
Citharichthys spilopterus
Bay whiff
Cynoscion nebulous
Spotted seatrout
Dorosoma cepedianum
Gizzard shad
Dorosoma pentenense
Threadfin shad
Fundulus simllis
Longnose killifish
Ictalurus furcatus
Blue catfish
0-4.9/- .
Leiostomus xanthurus
Membras martlnica
Rough silverside
Menidia beryl!ina
Tidewater silverside
Menticirrhus americanus
Southern kingfish
Micropogonias undulatus
Atlantic croaker
Mugil cephalus
Striped mullet
Paralichthys lethostigma
Southern flounder
Polydactylus ocfonemus
Atlantic threadfin
Prionotus tribulus
Bighead searobin
Sciaenops ocellatus
Red drum
Sphaeroides nephelus
Southern puffer
Synodus foetens
Inshore lizardfish
Trinectes maculatus
(from Perret et al. 1971)

estuaries on the way to spawning grounds. In the Gulf of Mexico, the
Alabama shad and the striped bass are important anadromous species
(Beccasio et al. 1982). Both species are sought for sport. Anadromous
species on the Pacific coast include Chinook salmon, chum salmon, pink
salmon, sockeye salmon, Dolly Varden, river lamprey and cutthroat trout
(Beccasio et al. 1981, Beauchamp et al. 1983). Studies have shown that
temperature is an important factor governing the timing of migrations and
spawning for some species. Chinook salmon (Oncorhynchus tshawytscha) will
not migrate when temperatures rise above 20F! American shad live most of
their lives at sea,- but pass through estuaries to spawn in fresh water.
Spawning of shad is dependent on temperature, and commences when the
maximum daily water temperature reaches 16C. It continues to about 24C,
peaking at 21C (Jones and Stokes Assoc. 1980). Additional information on
Pacific fishes is available in Hart (1973). Life history is presented
along with certain environmental requirements of the species. However,
salinity tolerances and preferences are noted infrequently.
Many of these anadromous species are major sport and commercial fish.
Striped bass, for exampl-e, occur along the east coast of North America from
the St. Lawrence River, Canada, to the St. Johns River, Florida; along the
Gulf of Mexico; and from the Columbia River, Washington to Ensenada,
Mexico, along the Pacific Coast (Bain and Bain 1982). Temperature was
cited as a key factor in their distribution. Striped bass migrate-to fres^i
or nearly fresh water to spawn. The optimum temperature for egg survival
is 17 to 20C. A minimum water velocity of 30 cm/s (1 fps) is necessary
to prevent eggs from resting on the bottom. After hatching, the larvae
remain in nearly fresh water. Striped bass- larvae need a minimum of 3 mg/1
dissolved oxygen. Optimum survival of larvae occurs when the temperature
is between 18C and 21C (12-23C tolerated) and. sal.inity ranges from 3-7
ppt (0-15 ppt tolerated). Juveniles are more tolerant of environmental
conditions and migrate to higher salinity portions of the estuary, feeding
on small prey fish. Optimum temperatures for juveniles are between 14C
and 21C, but a range of 10C to 27C can be tolerated. Some adult striped
bass may remain in estuaries, while others may embark on coastal migra-
tions. Striped bass populations from Cape Hatteras, North Carolina to New
England may travel substantial distances along the coast, while populations
in the southern portion of the range and on the Pacific Coast tend to
remain in the estuary or in offshore waters nearby (Bain and Bain 1982).
It should also be noted that preferred temperatures vary depending on
ambient acclimation temperatures. Striped bass acclimated to 27C in late
August avoided waters of 34C, while 13C was avoided by striped bass
acclimated to 5C in December.
Salmonids, numerous flatfJshes and sturgeon are dependent upon Pacific
coast estuaries at some time during their life cycles. For example, chum
salmon spawn in rivers from northern California to the Bering Sea during
October through December. Adults die after spawning. The young hatch in
spring, and move to estuaries and bays where they remain for 3 to 4 months.
They move to deeper waters gradually, as they grow (Beccasio et al. 1981).
The sand sole, a sport species along the northwest Pacific coastline,
spends up to its first year in bays and estuaries.
Some fish species utilize estuaries primarily as nursery grounds. Young-
fishes feed in the productive estuarine system and then migrate seaward or

Scientific Name
Alosa aestivalis
Alosa pseudoharenga
Brevoortia patronus
Brevoorti a tyrannus
Clupea harengus
Clupea harengus pallasii
Cottus asper
Cynoscion regal is
Lei ostomus~xanthurus
MicropogoniaTs undalatus
Morone americana
Morone saxatilis
Mugil cephalus
Mugi1 curema
Oncorhynchus gorbuscha
Oncorhynchus kisutch
Osmerus mordax
Platichthys stellatus
Pseudopleuronectes aroericanus
Salmo saTar
Tri nectes maculatus
(from U.S. EPA 1982, Jones and Stokes
et al. 1980) 
Common Name
Blueback herring
Alewi fe
Gulf menhaden
Atlantic menhaden
Atlantic herring
Pacific herring
Prickly culpin
Weakfi sh
Atlantic croaker
White perch
Striped bass
Mullet (striped)
Mullet (white)
Pink salmon
Coho salmon
Rainbow smelt
Yellow perch
Starry flounder
Winter flounder
Atlantic salmon
Assoc. 1981, Haedrich 1983, Beccasio
towards freshwater. Most of the fishes using estuaries as a nursery area
are anadromous, the adults being principally marine. Table I11-10 lists
anadromous fishes (from both the east and west coasts of North America)
which use estuaries primarily as nursery grounds. Although Table 111-10 is
not a comprehensive listing, it contains those fishes mentioned most
frequently in the literature (U.S. EPA 1983^, Jones and Stokes Assoc. 1981,
Haedrich 1983, Beccasio et al. 1980).
White perch (Morone americana), another commercially important fish, is
also abundant in estuaries on the east coast of North America. Populations
in the Chesapeake Bay area have been observed to inhabit the various
tributaries, with some fish entering the Bay itself. The American eel
(Anguilla rostrata) is the only catadromous species noted in the litera-
ture. It spawns in the Sargasso Sea, then migrates to and lives in
estuaries or freshwaters for several years before returning to the sea.
Some fish take advantage of the complex circulation pattern of estuaries,
spawning in offshore areas to allow eggs or larvae to drift up into the
estuary. Most notably, the young of flatfishes (winter and starry
flounder) and some of the drums (croaker, weakfish and spot) utilize the
estuarine circulation system (U.S. Dept. of Interior 1970). The juveniles
then feed and mature within the estuary." The gulf menhaden (Brevoortia

patronus) supports the largest commercial fishery by weight (Christmas et
aT"! 1982). It is an estuarine-dependent marine species that is found
primarily in northern Gulf of Mexico waters. Gulf menhaden spawn from
mid-October through March in marine waters. Currents transport planktonic
larvae to estuarine areas, where they transform into juveniles. As they
grow, juveniles migrate to deeper, more saline waters. Juveniles are able
to tolerate water temperatures from 5C to 34C. Adults and juveniles may
inhabit estuaries throughout the year. The Atlantic croaker also uses the
estuary as' a nursery area. Juveniles reside in salinities from 0.5 to 12
ppt, moving to higher salinity waters as they grow. They tolerate a wide
range of temperatures, from 6C to 20C. The spot (Leiostomus xanthurus)
is also estuarine dependent. Adults spawn in nearshore marine waters, but
juveniles spend much of their lives in estuaries. Juvenile spot tolerate
temperatures from 1.2C to 35.5C, preferring a range of 6C to 20C. They
have been collected in salinities from 0 to 60 ppt, but tend to concentrate
near the saltwater-freshwater boundary (Stickney and Cuenco 1982). Other
estuarine-dependent species in the Gulf of Mexico are the bay anchovy, sea
catfish, gafftopsoil catfish, spotted and sand seatrout, red drum, black
drum, southern kingfish and southern, flounder.
Some marine species enter the estuary seasonally. The spotted hake
(Urophycis regins) enters the Chesapeake Bay in late fall, and exits before
the warm weather. In Texas estuaries, Urophycis floridanus follows _a
similar migration pattern.
The bluefish (Pomatomus saltatrix) is often considered an adventitious
visitor to Atlantic coast estuaries (McHugh 1967). Although the bluefish
is a seasonal visitor, it may not appear if environmental conditions are
not suitable. Other species may occasionally enter estuaries to feed on
small fish, or if environmental conditions are suitable.
Difficulties often arise because sufficient information is not available on
the life cycles of certain species to enable their classification. For
this reason, and because of the many species of fish that enter estuaries
only occasionally, a fully comprehensive list of species is not available.
However, Haedrich (1983) compiled a listing of characteristic families
found in estuaries, based upon faunal lists reported in various papers. He
divided the fauna into families found in three zones, that of temperate,
tropics/subtropics, and high latitudes. The families in Table 111-11
include the few resident species, anadromous fish and marine species that
utilize the estuary as feeding and nursery areas.
Habitat Suitability Index Models
Habitat Suitability Index (HSI) models developed by the U.S. Fish and
Wildlife Service consider the quality of habitats necessary for specific
species during each life stage. The variables selected for study in a
given model are known to affect species growth, survival, abundance,
standing crop and distribution. Output from the models is used to
determine the quantity of suitable habitat for a species. The HSI values
produced by the models are relative, and should be used to compare two
areas, or the same area at different times. Thus, the area with the
greater HSI value is interpreted to have the potential to support a greater
number of a species than that with the lower HSI. Values range from 0 to

High Latitudes
Salmonidae (salmon and trout)
Osmeridae (smelt and capelin)
Gasterosteidae (sticklebacks)
Ammodytidae (sand lance)
Cottidae (sculpins)
* \
Temperate Zones
Anguillidae (freshwater eels)
Clupeidae (herrings)
Engraulidae (anchovies)
Ariidae (saltwater catfishes)
Cyprinodontidae (killifishes)
Gadidae (cods)
Gasterosteidae (sticklebacks)
Serranidae (basses)
Sciaenidae (croakers)
Sparidae (seabreams)
PIeuronectidae (flounders)
(from Haedrich -1983)
Tropi cs/Subtropi cs
Clupeidae (herrings)
Engraulidae (anchovies)
Chanidae (milkfish)
Synodontidae (lizardfish)
Belonidae (silver gars)
Mugilidae (mullets)
Polynemidae (threadfins)
Sciaenidae (crockers)
Gobiidae (gobies)
Cichlidae (cicheids)
Soleidae (flounders)
Cynoglossidae (flounders)
1, with 1 representing the most suitable conditions. HSI models can be
used to provide one value for all life stages, or to calculate HSI values
for each component (e.g. spawning, egg, larvae, juvenile, adult). There is
some uncertainty in the use of the HSI models, both in the form of cal-
culation and the fact that they are unverified models. They have not been
tested to see if they work. The form of calculation leads to the possi-
bility of their being insensitive to environmental changes. An area may
have undergone great degradation before the HSI model drops in value. More
information concerning HSI models can be found in Chapter IV-1 of the
Technical Support Manual (U.S. EPA 1983])). Models are currently available
for the following estuarine fish: striped bass (Bain and Bain 1982),
juvenile Atlantic croaker (Diaz 1982), Gulf menhaden (Christmas et al.
1982),	juvenile spot (Stickney and Cuenco 1982), Southern kingfish (Sikora
and Sikora 1982), and alewife and blueback herring (Pardue 1983). Models
have been developed for several other estuarine organisms. They are
northern Gulf of Mexico brown shrimp and white shrimp (Turner and Brody
1983),	Gulf of Mexico American oyster (Cake 1983), and littleneck clam
(Rodnick and Li 1983).
The preceding sections touch upon procedures that might be used and
specific phenomena that might be evaluated during the field collection
phase of a waterbody survey.
Strong seasonal changes in estuarine biological communities compound
difficulties involved in collection of useful data. Because of annual"
cycles, important organisms can be totally absent from the estuaries for

portions of the year, yet be dominant community members at other times.
For example, brown and white shrimp spend part of the year in estuaries,
and migrate to deeper, more saline waters as the season progresses.
Furthermore, estuarine biological communities may also vary from year to
year. Although it has not been mentioned explicitly, it is understood
that, if at all possible, a reference site will have been identified and
will have been studied in a manner that is consistent with the study of the
estuary of interest. In addition to whatever field data is developed on
the estuary and its reference site, it is also important to examine
whatever information might exist in the historical record.
The importance of submerged aquatic vegetation has not been fully discussed
in this Chapter, nor have any tools been presented by which to digest all
the assessments so far presented. This will be done in Chapter IV,

The basic physical and chemical processes of the estuary are introduced in
Chapter II, with particular emphasis placed on a description of stratifi-
cation and circulation in estuarine systems, on simplifying assumptions
that can be made to characterize the estuary, on desktop procedures that
might be used to define certain physical properties, and on mathematical
models that are suitable for the investigation of various physical and
chemical processes.
The applicability of desktop analyses or mathematical models will depend
upon the level of sophisticaton required for a particular use attainability
study. These types of analysis are important to the study in three ways: to
help segment the estuary into zones with homogeneous physical characteris-
tics, to help in the selection of a suitable reference estuary, and to help
in the analysis of pollutant transport and other phenomena in the study
area. Several case studies are presented to illustrate the use of measured
data and model projections in the use attainability study. The selection of
a reference estuary(ies) is discussed later in this Chapter.
Chapter II also offers a discussion of chemical phenomena that are partic-
ularly important to the estuary: the several factors that influence dis-
solved oxygen concentrations in surface and bottom layers and the impact of
nutrient overenrichment on submerged aquatic vegetation (SAV). Other chemi-
cal evaluations are discussed in the Technical Support Manual (EPA,
November 1983).
The biological characteristics of the estuary are summarized in Chapter
III. Specific information on various species common to the estuary are
presented to assist the investigator in determining aquatic life uses.
Typical forms of estuarine flora and fauna are described and the overall
importance of SAVs--as an indicator of pollution and as a source of habitat
and nutrient for the biotafor the use attainability study is emphasized.
In this Chapter, emphasis is placed on a synthesis of the physical,
chemical and biological evaluations which will be performed, to permit an
overall assessment of uses, and of use attainability in the estuary. Of
particular importance are discussions of the selection and analysis of a
reference site, and the statistical analysis of the data that are developed
during the use study.
There are many use classifications-navigation, recreation, water supply,
the protection of aquatic life-which might be assigned to a water body.
These need not be mutually exclusive. The water body survey as discussed in
this volume is concerned only with aquatic life uses and the protection of
aquaticU-fe in a water body.- Although the term "aquatic life" usually
refers only to animal forms, the importance of submerged aquatic vegetation

(SAV) to the overall health of the estuary dictates that a discussion of
uses include forms of plant life as well.
The use attainability analysis may also be referred to as a water body
survey. The objectives in conducting a water body survey are to identify:
1.	The aquatic life uses currently being achieved in the water body,
2.	The potential uses that can be attained, based on the physical,
chemical and biological characteristics of the water body, and
3.	The Causes are of any impairment of uses.
The types of analyses that might be employed to address these three points
are summarized in Table IV-1- Most of these are discussed in detail else-
where in this volume, or 1n the Technical Support Manual.
Use classification systems vary widely from State to State. Use classes
may be based on geography, salinity, recreation, navigation, water supply
(municipal, agricultural, or industrial), or aquatic life. Clearly, little
information is required to place a water body into such broad categories.
Far more information may be gathered in a water body survey than is needed
to assign a classification, based on.existing State classifications, but
the additional data may be necessary to evaluate management alternatives
and refine use classification systems for the protection of aquatic life in
the water body.
Since there may not be a spectrum of aquatic protection use categories
available against which to compare the. findings of the biological survey;
and since the objective of the survey is to compare existing uses with
designated uses, and existing uses with potential uses, as seen in the
three points listed above, the investigators may need to develop their own
system of ranking the biological health of a water body (whether qualita-
tive or quantitative) in order to satisfy the intent of the water body
survey. Implicit in the water body survey is the development of management
strategies or alternatives which might result in enhancement of the bio-
logical health of the water body. To do this it would be necessary to
distinguish the predicted results of one strategy from another, in cases
where the strategies are defined in terms of aquatic life protection.
The existing state use classifications may not be helpful at this stage,
for one may very well be seeking to define use levels within an existing
use category, rather than describing a shift from one use classification to
another. Therefore, it may be helpful to develop an internal use classi-
fication system to serve as a yardstick during the course of the water body
survey, which may later be referenced to the legally constituted use categ-
ories of the state.
A scale of biological health classes is presented in Table IV-2. This is a
modified version of Table V-2 presented in the Technical Support Manual,
and it offers general categories against which to assess the biology of an
estuary. The classification scheme presented in Table IV-3, which was
developed in conjunction with extensive. studies of the Chesapeake Bay,
associates biological diversity with various water quality parameters. The
Toxicity Index (Tj) in the table was discussed in Chapter III.
I V-2

(adapted from EPA 1982, Water Quality Standards Handbook)
Size (mean width/depth)
Total volume
Reaeration rates
Suspended solids
Bottom stability
Substrate composi-
tion and character-
i sties
Channel debris -
Riparian character-
i sties
 Dissolved oxygen
0 Toxics
-	nitrogen
-	phosphorus
0 Chlorophyll-a
 Sediment oxygen demand
0 Hardness
0 PH
"Dissolved solids
0 Biological inventory
(existing use analysis)
0 Fish
-	macroinvertebrates
-	microinvertebrates
0 Plants
-	phytoplankton
-	macrophytes
0 Biological condition/
health analysis
-	diversity indices
-	tissue analyses
-	Recovery Index
 Biological potential
analysi s
-	reference reach
compari son

IN WATER BODY ASSESSMENT (Modified from Karr, 1981)
Class	Attributes
Excellent	Comparable to the best situations unaltered by man;	all
regionally expected species for the habitat including	the
most intolerant forms, are present with full array of	age
and sex classes; balanced trophic structure.
Good	Fish invertebrate and macroinvertebrate species richness
somewhat less than the best expected situation; some
species with less than optimal abundances-or size dis-
tribution; trophic structure shows some signs of stress.
Fair	Fewer intolerant forms of plants, fish and invertebrates
are present.
Poor	Growth rates and condition factors commonly depressed;
diseased fish may be present. Tolerant macroinvertebrates
are often abundant.
Very Poor	Few fish present, disease, parasites, fin damage, and other
anomalies regular. Only tolerant forms of macroinverte-
brates are present.
Extremely Poor No fish, very tolerant macroinvertebrates; or no aquatic

CI ass Quality
A Healthy supports maximum
* diversity of benthic
resources, SAV, and
B Fair moderate resource
diversity, reduction
of SAV, chlorophyll
occasionally high
C* Fair a significant reduc-
to tion in resource
Poor diversity, loss of
SAV, chlorophyll
often high, occa-
sional red tide or
blue-green algal
D Poor limited pollution-
tolerant resources,
massive red tides or
blue-green algal
Very low
1-10 0.6-1.0- 0.08-0.14
11-20 1.1-1.8 0.15-0.20
Note: Tt indicates Toxicity Index
T* indicates Total Nitrogen in mg 1
\ y, iMUicaico iuiqi n i ii uycn hi my i
Tp indicates Total Phosphorus in mg 1
* Class C represents a transitional state on a continuum between classes
B and D.

Even though the estuary characteristically supports a lesser number of
species than the adjacent freshwater or marine systems, it may be consider-
ably more productive. Accordingly, uses might be defined so as to recog-
nize specific fisheries (and the different conditions necessary for their
maintenance), and. to recognize the importance of the estuary as a nursery
ground and a passageway for anadromous and catadromous species. Currently
the water body use classification systems of the coastal states distinguish
between marine and freshwater conditions, occasionally between tidal and
freshwater conditions, but seldom make reference to the estuary. Uses and
standards written for marine waters presumably are intended to apply to
estuarine waters as well.
It is common in these States to include as a use of marine or tidal waters
the harvesting and propagation of shellfish, frequently with reference to
the sanitary and bacteriological standards included in National Shellfish
Sanitation Program Manual of Operations: Part 1, Sanitation of Shellfish
Growing Areas, published by the Public Health Service .(1965). The term
shellfish applies to both molluscs and crustaceans. Other marine protec-
tion uses which may be applicable to the estuary are worded in terms such
as the growth and propagation of fish and other aquatic life, preservation
of marine habitat, harvesting for consumption of...raw molluscs _ or__other
aquatic life, or preservation and propagation of desirable species.
In establishing a set of uses and associated criteria to be used in the
water body survey, the investigator might wish to consider examples like
the State of Florida's criteria for Class II (Shellfish Propagation or
Harvesting) and Class III (Propagation and Maintenance of a Healthy, Wei 1 -
Balanced Population of Fish and Wildlife) Waters published in the Water
Quality Standards of the Florida Department of Environmental Regulation.
The published criteria are extensive and include the following categories
which are of importance to the estuarine water body survey:
Biological Integrity - the Shannon-Weaver diversity index of benthic
macroinvertebrates shall not be reduced to less than 75' percent of
established background levels as measured using organisms retained by a
U.S. Standard No. 30 sieve and collected and composited from a minimum
of three natural substrate samples, taken with Ponar type samplers with
minimum sampling areas of 225 square centimeters.
Dissolved Oxygen - the concentration in all waters shall not average
less than 5 milligrams per liter in a 24-hour period and shall never be
less than 4 milligrams per liter. Normal daily and seasonal
fluctuations above these levels shall be maintained.
Nutrients - In no case shall nutrient concentrations of a body of water
be altered so as to cause an imbalance in natural populations of
aquatic flora or fauna.

General Approach. There is a detailed discussion of the selection of
reference or control sites in Chapter IV-6 of the Technical Support Manual.
Although this discussion was prepared in the context of stream and lake
studies, much of the material is pertinent to the study of estuaries as
well. Riverine water body surveys may range in scale from a specific well-
defined reach to perhaps an entire stream. One might expect to find a
similar' range of scale in estuary studies. The lateral bounds of the
riverine study area generally are delineated by but not necessarily limited
to the stream banks. The specification of a reference reach is prescribed
by the scale of the study. If a short reach is under study, the reference
reach might be designated upstream of the study area. If an entire river
is under review, another river will have to be identified that will serve
as an appropriate control.
An estuarine study may focus on a specific area, but the bounds of the
study area are not easily defined because a physical counterpart to the
river bank may not exist. Other factors compound the difficulties in
designing an estuary study compared to the design of a river study. A
major difference is that estuary segments cannot be so easily categorized
because of seasonal changes in the salinity profile. Partitioning the
estuary into segments with relatively uniform physical characteristics is
an important first step of a water body survey.
It may be possible to study a small estuary as a single segment, but it
will be necessary to go elsewhere for a reference site. This may be easily
accomplished among the many bar built estuaries of the southeastern coast.
For the large estuary, one may need only to examine a well-defined segment
which has been affected by a point source discharge. If the segment is an
embayment tributary to the main stem of the estuary, it may not be diffi-
cult to find a suitable control embayment within the same estuary. As the
scale of the study increases, however, the difficulties associated with the
establishment of a reference site also increases. It may 'not make sense to
treat the entire estuary as a single unit for the use attainability survey,
especially if use categories are associated with salinity ranges, different
depths, etc. In such a case one .would segment the estuary based upon
physical characteristics such as salinity levels and circulation patterns,
and then define the reference site in similar fashion. As a practical
matter, it may not make sense to examine an entire estuary as a single
unit, especially a large one. For example, the Chesapeake Bay has been
subjected to a form of use attainability studies for a number of years at a
cost of many millions of dollars. However, Chesapeake Bay is so complex
that, despite the intensity of study, clear explanations are not always
possible for the many undesirable changes that have taken place. The
Chesapeake- Bay itself is unique and no suitable reference estuary exists.
From the use attainability standpoint, an estuary such as the Chesapeake or
the Delaware or the Hudson is best broken down into segments that are
homogeneous in characteristics and manageable in size.
Statistical Comparisons of Impact Sites With Control Sites. Reference site
comparisons typically rely upon either parametric or nonparametric statis-
tical tests of the null hypothesis to determine whether water quality or

any other use attainment indicator at the impact site is significantly
different from conditions at the control site(s).
Parametric statistics, which are suitable for datasets that exhibit a nor-
mal distribution, include the F (folded)-statistic on the difference be-
tween the variances at the impact site and control site and the t-statistic
on the difference between the means. In order to conclude that there is no
significant difference between the water quality conditions (or another
indicator) at'the impact site and the control site, both the F-statistic
and the t-statistic should exhibit probabilities exceeding the 0.05 prob-
ability cutoff for the 95 percent confidence interval. In cases where the
impact site is being compared with multiple control sites, parametric pro-
cedures such as the Student-Newman-Keuls (SNK) test, the least significant
difference (LSD) test, and the Duncan's Multiple Range test can be used to
test for differences among the grouped means.
Since water quality datasets are often characterized by small sample sizes
and non-normal distributions, it is likely that nonparametric statistical
tests may be more appropriate for the monitoring database. Nonparametric
statistics assume no shape for the population distribution, are valid for
both normal and non-normal distributions, and have a much higher power than
parametric statistical techniques for analyses of datasets which are char-
acterized by small sample sizes and skewed distributions. The one-sided
Kolmogorov-Smirnov (K-S) test can be used to quantify whether each dataset
is normally (or lognormally) distributed, thereby governing the selection
of either parametric. or nonparametric procedures. If nonparametric pro-
cedures are selected, significant differences in distributions can be
evaluated with the two-sided K-S test, while significant differences, in the
central value can be tested with the Wilcoxon Ranksum test. Both nonpara-
metric tests should exhibit probability values exceeding the cutoff for the
95 percent confidence interval in order to conclude that there is no signi-
ficant difference in water quality conditions at the impact site and a con-
trol site. For comparisons with multiple control sites, nonparametric pro-
cedures such as the Kruskal-Wallis test and the Friedman Ranksum test can
be used to test for significant differences among medians (if it can be
assumed that the distributions of each dataset are not significantly
di fferent.
The same types of statistical tests can be used to evaluate sediment and
biological monitoring data to determine whether suitable conditions for use
attainability exist at the impact site. Either parametric or nonparametric
statistical procedures can be used to compare conditions at the impact site
and control site(s) which are unaffected by effluent discharge or other
pollution sources. In cases where there are no statistically significant
differences in distributions and/or control values, it may be assumed that
sediment and/or biological monitoring results at the impact site and con-
trol site(s) are similar.
The actual aquatic protection uses of a water body are defined by the resi-
dent flora and fauna. The prevailing chemical and physical attributes will
determine what biota may be present, but little need be known of these at-
tributes to describe current uses. The raw findings of a biological survey

may be subjected to various measurements and assessments, as discussed in
Section IV (Biological Evaluations) of the Manual. After performing an
inventory of the flora and fauna and considering a diversity index or other
indices of biological health, one should be able adequately to describe the
condition of the aquatic life in the water body.
If the biological evaluations indicate that the biological health of the
system is impaired relative to a "healthy" reference aquatic ecosystem
(e.g., as determined by reference site comparisons), then the physical and
chemical evaluations can be used to pinpoint the causes of that impairment.
Figure IV-1 shows some of the physical and chemical parameters that may be
affected by various causes of change in a water body. The analysis of such
parameters will help clarify the magnitude of impairments to attaining
other uses, and will also be important to the third step in which potential
uses are examined.
A third element to be considered is the assessment of potential uses of the
water body. This assessment would be based on the findings of the physi-
cal, chemical and biological information which has been gathered, but addi-
tional study may also be necessary. A reference site comparison will be
particularly important. In addition to establishing a comparative baseline
community, defining a reference site can also provide insight into the
aquatic life that could potentially exist if the sources of impairment were
The analysis of all information that has been assembled may lead to the
definition of alternative strategies for the management of the estuary at
hand. Each such strategy corresponds to a unique level of protection of
aquatic life, or aquatic life protection use. If it is determined that an
array of uses is attainable, further analysis which is beyond the scope of
the water body survey would be required to select a management program for
the estuary.
One must be able to separate the effects of human intervention from natural
variability. Dissolved oxygen, for example, may vary seasonally over a
wide range in some areas even without anthropogenic effects, but it may be
difficult to separate the two in order to predict whether removal of the
anthropogenic cause will have a real effect. The impact of extreme storms
on the estuary, such as Hurricane Agnes on the Chesapeake Bay in 1972, may
completely confound our ability to distinguish the relative impact of
anthropogenic and natural influences on immediate effects and longterm
trends. In many cases the investigator can only provide an informed guess.
Furthermore, if a stream does not support an anadromous fishery because of
dams and diversions which have been built for water supply and recreational
purposes, it is unlikely that a concensus could be reached to restore the
fishery by removing the physical barriers -- the dams -- which impede the
migration of fish. However, it may be practical to install fish ladders to
allow upstream and downstream migration. Another example might be a situ-
ation in which dredging to remove toxic sediments may pose a much greater





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Riparian Characteristics










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. C
Figure IV-1.
Potential Effects of Some Sources of
Alteration on Water Quality Parameters;
D = Decrease, I = Increase, C = Change

threat to aquatic life than to do nothing. Under the do nothing alterna-
tive, the toxics may remain in the sediment in a biologically-unavailable
form, whereas dredging might resuspend the toxic fraction, making it
biologically available and also facilitating wider distribution in the
water body.
The points touched upon above are presented to suggest some of the phenom-
ena which may be of importance in a water body survey, and to suggest the
need to'recognize whether or not they may realistically be manipulated.
Those, which cannot be manipulated essentially define the limits of the
highest potential use that might be realized in the water body. Those that
can be manipulated define the levels of improvement that are attainable,
ranging from the current aquatic life uses to those that are possible with-
in the limitations imposed by factors that cannot be manipulated.
Uses that have been impaired or lost in an estuary can only be restored if
the conditions responsible for the impairment are corrected. Impairment
can be attributed to pollution from toxics or overenrichment with nutri-
ents. Uses may also be lost through such activities as the disposal of
dredge and fill materials which smother plant and animal communities,
through overfishing which may deplete natural populations, the destruction
of freshwater spawning habitat which will cause the demise of anadromous
species, and natural events in the sea, such as the> shifting of ocean
currents, that may alter the migration routes of species which visit the
estuary at some time during the life cycle. One might expect losses due to
natural phenomena to be temporary although man-made alterations of the
estuarine environment may prevent restoration through natural processes.
Assuming that the factors responsible for the loss of species have been
identified and corrected, efforts may be directed towards the restoration
of habitat followed by natural repopulation, stocking of species if habitat
has not been harmed, or both. Many techniques for the improvement of sub-
strate composition in streams have been developed which might find applica-
tion in estuaries as well. Further discussion on the importance of sub-
strate composition will be found in the Technical Support Manual (EPA,
November 1983).
Stocking with fish in freshwater environments, and with young lobster in
northeastern marine environments, is commonly practiced and might provide
models for restocking in estuaries. In addition, aquaculture practices are
continually being refined and the literature on this subject (Bardach et
al., 1972) should prove helpful in developing plans for the restoration of
estuaries or parts of estuaries.
Submerged aquatic vegetation -(SAV) is considered to be an excellent indica-
tor of the overall health of an estuary because it is sensitive to environ-
mental degradation caused by physical smothering, nutrient enrichment and
toxics. Because SAV is s-o important as habitat and as a source of nutrient
for a wide range of the estuarine biota, its demise signals the demise of
its dependent populations. If uses in an estuary have been impaired or
lost, it is likely that SAV will also have been affected.

Unfortunately, the cause of SAY degradation is not always clear. In the
Chesapeake Bay for instance, controversy persists as to the cause of loss
of SAV and the loss of biota which depend to whatever extent on SAY.
Trends noted over time in the demise of these populations may conceivably
be related to trends in toxic, sediment and nutrient loadings on the Bay,
and to trends 1n the release of chlorinated wastewaters from POTWs, chlor-
inated effluents from industry and chlorinated cooling water from power-
plants. Areas in which SAV has been adversely impacted are areas where
there are toxics in the sediment and/or where algal blooms prevent light
from reaching SAV communities.
The ability to restore areas of SAV will depend upon the initial causes of
loss, and the ability to remove the causes. Toxics in sediment may be a
particularly difficult problem because of the impracticality of dredging
large areas to remove contaminated bottom substrate. An inabilty to remove
toxic sediments which may have caused a decline in SAV and other benthic
communities severely limits the likelihood that these populations may be
restored to past levels.
The control of nutrients may be a much more tractable problem. If nutrient
Inputs to the estuary can be controlled, SAV populations may begin to ex-
pand on their own. In the Potomac River estuary, phosphorus removal at the
Blue Plains wastewater treatment plant, which serves the greater Washings
ton, D.C. area, has resulted in sharp reductions in algal blooms which are
considered a major factor in the demise of SAV within the Chesapeake Bay
Apart from natural processes which result in the enlargement of areas of
SAV, SAY may be restored through reseeding and transplanting, depending
upon the species. Generally speaking, reseeding may not be a. practical
approach because of the cost of collecting seeds and because one would not
expect all seeds to survive, although Vallisneria (wild celery) shows some
promise in using seeds to reestablish populations. Some areas may reseed
naturally, but in many cases SAV populations may be too distant for the
natural transport of seeds to be likely. In these cases, plants may be
transplanted In order to restore SAV. Reestablishment is accomplished by
transplanting shoots and rhizomes.
Although transplanting may be a more-practical alternative, the outcome is
not assured. In an effort to reestablish SAV, plugs of Zostera (eelgrass)
and Potamogeton (sage pondweed, redhead grass) were planted in the Potomac
River estuary. These beds showed some measure of success, depending mainly
upon the substrate present. The transplanting of SAV is a labor intensive
operation and-as such would require a considerable cost in time and re-
sources to restore even a small area.
In Tampa Bay, Florida, stress on the ecosystem, including the disposal of
dredge spoils which have smothered SAV communities, has caused a signifi-
cant loss (25,220 ha, or 81 percent) of submergent wetland vegetation. Ef-
forts to reestablish Spartina (cord grass) and Thalassia (turtlegrass) have
resulted in the restoration of about 11 ha of vegetation (the growth and
spreading of rhizomateous material is increasing this figure) (Hoffman et
al., 1982). The transplantation of Thalassia and Halodule (shoalgrass)
near the discharge side of a powerplant was less successful, in that

Thai as si a failed to survive for 30 days where the mean watei? tsmpjeratare
was 31 C or greater, and only small patches of shoalgrass survived: near tfche
outer edges of the thermal plume. These differences coildi no# b.e aittri-
buted to differences in sediment composition (Blake et al., I'rEVrh Nta^r-
theless, other transplantation efforts emphasize ths ini^arijarrc. f
substrate to plant survival. For example, Thalassia prefers; a, reduced
environment while Halodule prefers an oxidized substrate.
Transplanting' oyster spat from "seed" areas which are pro.te.te(L firanr har-
vesting to areas less favorable for reproduction is a re1!aHi:v.el!y csminraffl
practice. Seed areas ideally exhibit optimum salinity ani> temper&Sur: for
oyster reproduction and spat set. Clean shell is deposited as substrate fiim
seed areas and spat often become very densely populated. Spa.t are- Uttem
moved to areas where an oyster population is desired. Steps, may, alls '&e
taken to prepare the bottom (often by depositing oyster shaiVTs) wheitu ami
oyster reef exists, or where attempts will be made to estab-Tfstt ans ouster
Although there has been some progress in the aquacultural s
Addy, C.E. and D.A. Aylward. Status of eelgrass in Massachusetts during
1943. J. Wildl. Mgr. 8:265-275, 1944.
Adkins, G. and P. Bowman. A study of the fauna in dredged canals of
coastal Louisiana. La. Wild!. Fish Comm. Tech. Bull., 18:1-72, 1976.
Adkins, G., J. Tarver, P. Bowman, and B. Savoie. A study of the commerical
finfish in coastal Louisiana. La. Dep. Wildl. Fish., Seafood Div. Tech.
Bull., 29:1-87, 1979.
Ahlstrom, E.H., et al. Sampling zooplankton to determine biomass. In:
Recommended procedures for measuring the productivity of plankton
standing stock and related oceanic properties, E.H. Ahlstrom (ed.),
Washington, D.C., National Academy of Sciences, 1969.
Alheit, J. and W. Schneibel. Benthic harpacticoids as a food source for
fish. Marine Biology 70:141-147, 1982.
Allen, L.G. and M.H. Horn. Abundance, Diversity and Seasonality of Fishes
in Colorado Lagoon, Alamitos Bay, California. Estuarine and Coastal
Marine Sci. 3:371-380, 1975.
Ambrose, R.B., T.O. Najarian, G. Bourne, and M.L. Thatcher. Models for
Analyzing Eutrophication in Chesapeake Bay Watersheds: A Selection
Methodology. EPA, Chesapeake Bay Program, Annapolis, MD, 1981.
American Public Health Association. National Shellfish Sanitation Program
Manual of Operations: Part 1, Sanitation of Shellfish Growing Areas.
Anderson, R.R. Ecology and Mineral Nutrition of Myriophyl1um spicatum
(L.). M.S. Thesis, Univ. Maryland, College Park, 1964.
Anderson, R.R. Submerged vascular plants of the Chesapeake Bay and
tributaries. Chesapeake Sci. 13(suppl.):S87-S89, 1972.
Anderson, R.R. Temperature and rooted aquatic plants. Chesapeake Sci.
10(3 and 4):157-164, 1969.
Anderson, . R.R., R.G. Brown-, and R.D.  Rappleye. Mineral composition of
Eurasian water-milfoil, Myriophyllum spicatum. Chesapeake Sci.
6(1 ):68-72, 1965.
Anonymous. Creeping and crawling on Currituck Sound, the dilemma of
Eurasian watermilfoil. Univ. North Carolina Sea Grant News Letter, 1976.
Arasaki, M. The ecology of Amamo (Zostera marina) and Koamamo (Zostera
nana). Bull. Jap. Soc. Sci. Fish. 15:5b/-572, 19b0a^

Arasaki, M. Studies on the ecology of Zostera marina and Zostera nana.
11. Bull. Jap. Soc. Fish. 16:70-76, 1950b/
Arnold, C.R., T.D. Williams, W.A. Fable, Jr., J.L. Lasswell, and W.H.
Bailey. Methods and Techniques for Spawning and Rearing Spotted Seatrout
in the Laboratory. Proc. Annu. Conf. Southeast. Assoc. Game Fish Comm.
30:167-178, 1978.
Auld, A.H. and J.R. Schubel. Effects of Suspended Sediment on Fish Eggs
'and Larvae: A Laboratory Assessment. Estuarine Coastal Mar. Sci.
6:153-164, 1978.
Backman, T.W. and D.C. Barilotti. Irradiance reduction: effects on
standing crops of the eel grass Zostera marina in a coastal lagoon. Mar.
Biol. 34:33-40, 1976.
Bain, M.B. and J.L. Bain. Habitat Suitability Index Models: Coastal
Stocks of Striped Bass. U.S. Dept. Int. Fish Wild!. Serv., Washington,
D.C. FWS/OBS-82/10.1, 1982.
Baker, F.C. The productivity of invertebrate fish food on the bottom.of
Oneida Lake, with special reference to mollusks. New York State College
of Forestry, Syracuse Univ. Tech. Pub. No. 9 18(2), 1918.
Bardach, J.E., J.H. Ryther, and W.O. McLarney. Aquaculture - The Farming
and Husbandry of Freshwater and Marine Organisms. Wiley-Interscience,
New York, 1972.
Barger, L.E., L.A. Collins, and J.H. Finucane. First record of bluefish
larvae, Pomatomus saltatrix, in the Gulf of Mexico. Northeast Gulf Sci.
2(2):145-147, 1978.
Beal, E.O. A manual of marsh and aquatic vascular plants of North Carolina
with habitat data. Tech. Bull, of the North Carolina Agric. Exp. Sta.
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To assess the contribution of anthropogenic sources of metal contamination
over"time,- sediment cores may be analyzed. The Wedepohl ratio compares the
amount of metal in the sediment sample with the concentration in an average
shale (or sandstone). In the Chesapeake Bay program, scientists have
measured silicon and aluminum, then correlated metals with Si/Al ratios. A
contamination factor (Cf) may be computed as follows:
Cf = (Co-Cp)/Cp
where: Co = surface sediment concentration
Cp = predicted concentration, derived from the statistical
relation between the Si/Al ratio and the log metal content of
old, pre-pollution sediments from the estuary.
Thus, Cf < 0 when the observed metal concentration is less than the pre-
dicted value; Cf = 0 when observed and predicted are the same; Cf > 0 when
the observed is greater than the predicted value.
The Corrtamination Index (C,) is found by summing contamination factors for
metals in a given sediment.
n	n
CT "= ItL Cf = 2 (Co-Cp)/Cp
L n=l	. n=l
The Toxicity Index (T.) is related to the Contamination Index and is
expressed by the following equation:
where: M. = the "acute" anytime EPA criterion for any of the metals,
but	is always the criterion value for the most toxic of the metals.
The "acute" anytime EPA criterion is defined as the concentration of a
material that may not be exceeded in a given environment at any time. When
evaluating .Toxicity Indices, sampling stations should be characterized by
their minimum salinities. This is because the toxicity of metals is often
greater in freshwater than in saltwater.
A more detailed discussion of the development of the Contamination Index
may be found in the-U.S. EPA publication, Chesapeake Bay: A Profile of
Environmental Change (1983a) and A Framework for Action (1983c).

1. General Fishery Information
a.	Alosa aestivalis (Blueback Herring)
b.	Alosa pseudoharengus (Alewife)
c.	Alosa sapidissima (American Shad)
d.	Brevoortia tyrannus (Atlantic Menhaden)
e.	Callinectes sapidus (Blue Crab)
f.	Crassostrea virginica (American Oyster)
g.	Cynoscion regalis (Weakfish)
h.	C. nebulosus (Spotted Seatrout)
i.	Ictalurus catus (White Catfish)
j.	Ictalurus nebulosus (Brown Bullhead)
k.	Ictalurus punctatus (Channel Catfish)
1.	Leiostomus xanthurus (Spot)
m.	Mercenaria mercenaria (Hard Clam)
n.	Micropogonias undulatus (Atlantic Croaker)
o.	Morone americana (White Perch)
p.	Morone saxatilis (Striped Bass)
q.	Mya arenaria (Soft Shell Clam)
r.	Perca flavescens (Yellow Perch)
6.	Pomatomus saltatrix (Bluefish)
(from U.S.EPA 1983a_)

Tidal-fresh and low-
brackish water.
Egge arc found in
streams and rivera
with awift currenta
and sandy or rocky
Not applicable
No information
Not applicable
No information
Burbidge 1974
Hudson and Hardy 1974
Jonea et al. 1978
Li'ppaon et al. 1979
Tidal-freah and
brackiah water*
Larvae are found in
tributary atreams and
upper portiona of
Optimum salinity
0-5 ppt.
- copepoda 
Growth occurs
during warn tem-
Interspec ific
competition with
Bay anchovy in
brackish water
causes larvae to
select food items
other than the
preferred type.
Compete with Bay
Prey of predatory
fiah (striped bass,
white perch)
Domermuth and Reed
Raney and Massmann
Tidal-freah and
brackish water.
Juveniles are found
primarily in aurface
Tolerate salinity
0-28 ppt.
Optimum salinity
0-5 ppt.
Selective feeder
during daylight.
-	copepods
-	copepodites
-	Bosraina spp.
-	macroiooplankton
Growth occurs
during warm tem-
peratures; rate of
growth is more
rapid than for
Young juvenilea
remain in nuraery
area until the
fal Ip then under-
take a seaward
migration. Young
may remain in the
lower Bay during
first or second
Prey of predatory
fish (striped baaa,
white perch,

Adul C
0-34 ppt salinity.
Adults- enter the Bay
to spawn in fresh-
water; return to the
ocean after spawning.
-	zooplankton
-	crustaceans
-	crustacean eggs
-	insects
-	fish egga and
Blueback herring
mature in 3-4 yrs.,
and reach a maxi-
mum length of 38.0
Schooling herring
occur in a narrow
band of coastal
water; move to the
bottom during winter*
Herring are ana-
drexsoua, migrating
into the Bay to
Prey of predatory
fish (striped
bass, bluefish,
weakfish) in fresh,
brackish, 4 salt
water. Target of
m commercial 4
recreat ional

(pawn in (pring.	fishery.

0-0.5 ppt aalinity.
Eggs are released in
slow, shallow
portions of creek*
and rivers over
detritus ot sandy
Not applicable
Hatching period 6
days. Hean water
temp.- 60F.
Hot applicable
No information
Jones et al. 1978
Shea at al. 1980
Lippaon et al. 1979
Hildebrand and
Schroeder 1928
0-3 ppt salinity.
Larvae remain in
vicinity of spawning
area at depths leas
than 3m.
-	rotifers
-	copepod nauplii
No information
Form schools
within 1-2 dsya
after hatching.
Prey of predatory
fish (white perch
and atriped baaa)

Tolerate salinity
0-34 ppt.
Optimum salinity
0.5-5 ppt.
Juvenile Young juvenile* ire
found in nursery
areaa from shore to
shore; as the fish
grow, there is a slow
downstream movement
- copepoda
myaid shrimp
Grow very rapidly,
possibly due to
entering salt water,
average 105 na.
Young juveniles
migrate toward the
ocean in the fall,
some overwinter in
deep areas of the
Prey of predatory
fish (bluefish,
striped baas, white
0-34 ppt salinity.
Adults enter the
Adult	Bay to spawn in
freshwater; return
to ocean by mid-
Mid-water feeder
-	copepods
-	young fish
-	zooplankton
-	aysids
Alewife nature in
3-4 yrs., measuring
an average 25.0-30.0
cm in length.
Schooling alewife
ahow regular
anadroaous Alosid
coastal movements.
Alewife are ana-
dromous, migrating
into the Bay to
spawn in spring.
Prey of predatory
fish (striped
baaa, bluefish,
veakfiah). In
fresh, brackish,
and salt water.
Target of commer-
cial and recrea-
tional fiahery.



0-0.3 ppt salinity.
Streams and riven
with swift current!
and sandy or rocky
Not applicable
Temperatures above
2lC and low D.O.
level* decrease
hatching iucceii
Not applicable
Ho information
Hildebraod and
Schroeder 1928
Shaa et cl. 1980
Dosenauth and Iced

Optinun aalinity
0-5 ppt.
Larvae are found at
deptha greater than
No information
Ac D.O. level* of
5 ppfi, tome stress-
and mortality occurs;
at 0.0. levela of
U ppa, high mortality
ay occur.
No information
Preyed upon by top
predatory species
(striped bass,
bluefish, white
perch, other herring
Lippaoo el al. 1979
Cilia et al. 1947
Tolerate aalinity
0.5-12 ppt.
Optimum salinity
5-12 ppt.
Young juvenilea
gradually nove into
aiore aaline waters.
Feed at or
beneath surface
-	dsphnid clado-
-	boaminid clado-
-	other cladoceran
-	copepoda
Young grow rapidly
during the firat
Juvenile* regain
in natal atream
and rivera until
the fall, then
undertake a seaward
migration* Sooe
reaain in the lover
Bay during the
firat winter*
Competition with
species such aa
the alewife or
blueback herring
influence location
of feeding fiah 4
aelection of prey.
Prey of top preda-
tory species.


P-J& BP1.
fclnlf t"H*r 8it
t gpa4H ifl ft**'1"
w^er ut pn iw
t id** VS^r1; refUF?
to ocg.n jfjjf
Feed in aurface
1 ? * S f
 bui.!! 11 M*.h
t a
Crowth rate de-
cicie a I ^ c r 3

HOf.t> #),
Tiflf f 
U6Bll 1 t


_ 	:I
the ocean, probably
Egg*	not far (aa far 
64 km) from the
mouth of the Bay.
Not applicable
No information
Early larvae tolerate
18-34 ppt salinity.
Larvae	Optimum aalinity
25-34 ppt. Later
they concentrate in
tidal fresh to low
brackish waters
(0-3 ppt salinity).
- copepods
size of fish
influencea sice
of copepods
No information
Larvae enter the
Bay in apring when
they are about 10-30
B*a long; nay reach
nursery areaa in
larval ar juvenile
Ho information

Tolerate aalinity
Filter feeder
No information
Prey of top preda-

0-34 ppt.
- phytoplankton

juveniles remain
tory fish including
Optimum salinity
0-15 ppt. Younger
fish concentrate in
tidal-fresh to low-
brackish waters.

in the Bay during
Sumner; msy leave
in fall or over-
winter in Bay.
bluefish and atriped
Tolerate aalinity
1-36 ppt concentrate
in areas of 5-18 ppt
Adult	salinity where food .
patched occur. One
and two year old
adults utilize the
Bay; older fish
remain off the
Filter feeder
-	zooplankton
-	larger phyto-
-	longer chains
of chain-
forming diatoms.
Feeding behavior
is linked to food
density and par-
ticle size.
maturity in one year;
all fish are mature
by age 3. Haximum
length around 47.0
Schooling marine
fish which enter
the Bay in apring
to feed; moat
migrate seaward in
the fall, though
some may overwinter
in the lower Bay.
Prey of top pre-
datory fish in-
cluding bluefish
nd striped bass.
Target of a com-
mercial fishery.
Shea ct a1. 1980
June and Carlaon 1971
Durbin and Durbin 1975
Lippaon ec ai. 1979



Hatch at salinities
of 10.3-32.6 ppt;
optimum salinities
for hatch are 23-30
ppt. Female* carry
the egg* until hatch
Not applicable
Salinity affect*
hatching success.
Not applicable
No information
Van Engcl c al. 1973
Shea tt al. 1980
Sulkin 1)75
Van Engel 1958
Tolerate aalinitiea
of 15.8-32.3 ppt;
optimum aalinitiea
are 21-28 ppt.
Zoeae are found in
the upper aurface
-	rotifer*
-	Nauplii larva*
-	tea urchin
-	polychaet*
Zoeae molt at leaat
three time*, with
the final mold pro-
ducing a megalopa.
Molting is affepted
by salinity, temper-
ature, larval con-
centrations, nd
light intensity.
Zoeae ahow an
attraction to
i ight.
No information
Sandoc and Roger* 1944
Lippaon 1971
Lippson et al. 1979

Optimum salinities
of 20-35 ppt. Mega-
lop* oiay be found in
*urface water* or on
the bottom.
-	plant*
-	fish and ahell-
fish piece*
-	detritus
Avaliability of
prey affect* diet.
Salinity and temper-
ature affect the
durat ion of the
oegalops stage.
Megalops metamorphose
into a small juvenile
Hegalop* and juven-
iles move int9 the
Bay through the
entrainment in bottoa
waters, beginning in
fall. In winter
young crabs cease
migrations and burrow
into channel bottom*.
No information

Adu It*
Juveniles concentrate
in bracki*h water
with aalinitiea lea*
than 20 ppt. Adult
males concentrate
in lalinitie* of
3-15 ppt. Female*
concentrate in
alinitiea of 10-28+
-	benthic organ-
-	mall fish
-	plant*
-	shellfish
-	small crust-
-	detritua
Availabi1ity of
prey affecta diet.
Crabs reach sexual
maturity in 12-20
months depending on
t iming of hatch.
Growth occurs by
hedding the (hell,
and i* regulated by
water temperature.
In warm weather,
juveniles move in-
shore. Uhen temper-
ature* drop, juven-
iles move to channel
area* to overwinter
in semi-hibernation.
Adult* have aimilar
movement pattern*.
-	predatory fish
such a* striped
bass snd bluefish
-	birds such as
herons and herring
-	a commercial and
recrest iona1

Optimum aalinity of
22.5 ppt; below 10
ppt, survival ia poor.
Pelagic eggi releaaed
in open water.
Not applicable
Turbidity levela of
12 5 tr.g L~* or more
reduce development
and aurvival of
Not applicable
No information
Caltaoff 1964
Haven and Horatea-
Alamo 1970
Korrlnga 19)2
Juvenile t
Optimal growth occur#
C salinities of
12.5-25.0 ppt.
Filter feeder
-	phytoplankton
-	bacteria
The size of food
particles taken is
a function of the
south site.
Turbidity levels of Oyster larvae
100 sig L~1 cause	nove within the
high larval mortality* estuary by entrain-
Prey of planktomc-
feeding fish and
Salinity, tempera-
ture, and available
food influence
larval development
ment in bottom
waters. Larvae search
for suitable substrate
on which to attach
in about two weeks.
At setting, larvae
metamorphose tp spat*
Salinity 5-35 ppt.
Oysters are found
in shallow water less
than 10 meters deep.
Optimum survival of
oysters occurs on
hard substrate such
as rocks, pilings,
and oy9ter shells in
the intertidal and
sub-tidal zones*
Filter feeder
-	phytoplankton
-	bacteria
-	detritus
Spat exhibit rapid
growth during the
first year. Growth
rates are affected
by availability of
food, salinity, and
water temperature.
Oyste ra initially
develop as males,
yet by the second
breeding sesson
many change into
Filter feed on
112 micron prey
-	phytoplankton
-	bacteria
-	detritus
Turbidity and low
temperatures in-
fluence feeding
and digestion.
Growth is affected
by substrate type,
salinity, tempera-
ture, tidal flow,
and crowding. Oysters
reach sexual maturity
during the' second
year of growth. (A
few reach maturity
at one year CHaven))
Epibenthic with
frequent alternation
of sex. Form com-
munities or "bars."
Oyster distribution
in higher sslinity
areas is restricted
by predators and
-	boring sponges
and clams
-	slipper shell
-	sea squirt
-	barnaples
-	spirochaetes
-	perforating
-	oyster drills
-	blue crabs
-	starfish
-	bi rds
-	commercial fishery
-	Perkinsus marinus
-	Menchinia nelsoni
Davis and Calabrese
Ukeles 1971
Andrews 1967, 1968
Haven, personal
comounicat ion

Tolerate salinities
of 5-34 ppt.
Buoyant egga are re-
leaaed in Che near-
ahore and eatuarine
tones along the coaat.
Not applicable
Egg* are susceptible
to low D.O. levels
and sudden changes
in either salinity
or temperature.
Not applicable
No information
Lippson et al. 1979
Daiber et al. 1976
Uilk 1978
HcHugh 1978
Tolerate aalinitica
12-31 ppt.
Larvae remain in the
general vicinity of
No information
Larvae cannot with- No information
atand sudden changes
in either salinity or
temperature; a 5C
change in temperature
in either direction can
be fatal.
No information

About 0-34 ppt
salinity. Young-of-
the-year fish move
into low salinity
treat over soft.
Buddy bottoms.
-	shrimp
-	other crust-
acean spp.
-	bay anchovy
-	young menhaden
-	other small fish
Vleakfish grow most
rapidly during their
first year, reaching
an average length of
19 cm.
Young juveniles move
into low aalinity
areaa for the aunaer;
migrate to the coast
in fall, and move
offshore and south in
the winter. Begin
schooling aa pre-
Preyed upon by
bluefish, striped
bass, and large

Adu Ic
Tolerate salinities
of 10-34 ppt.
Adults remain in the
lower portion of the
Primarily pisci-
-	menhaden
-	herring spp.
-	bay anchovy
-	silveriide*
r c run L a;.* (lua
Weakfish are aexually
mature in 2-3 years,
and reach an average
length of about 50.0
Adults school, arrive
in Bay in spring,
leave by late fall
and head south and
offshore for the
tq lnihofe areas '
in sprang.
Preyed upon by
bluefish and
striped bass.
The target of a
commercial and


Spavming occurs at

Eggs are susceptible

Tabb 1961
salinities of 30-35

to low D.O. and sudden

Egg* ppt- Hatched in 40
Not applicable
changes in salinity'
Not applicable
No information Arnold ct al. 1978
hra at 25C.

or temperature.

Eggs reported as

Fable et al. 1978
both demersal and

pelagic, re leased

Idyll and Fahy 1975
in deeper channels

and holea adjacent

Lorio and Perret
to grassy bays and


Growth of larvae
Very small in-
Highly sensitive to
Tend to remain

is rapid, about
ve rt ebrates,
changes in tempera-
close to site

including cope-
ture. Uinter-t ime
dt spawning
No information
after hatching.
pods, mygid
cold, shock andhigh
in grassy

Young fish spend
shrimp, and post-
temperature changea

their juvenile
larval penaeid
causes kills.

life in vegetated

f lata, moving to

deeper water in


Fish larger than
As the trout grow.
Females grow faster
Start to
Reported as
2 inches show a
diet changes to
than males but males
school as
highly can-
Juvenile tendency to con-
include larger por-
attain sexual maturity
young fish
nibal i st ic
gregate in schools.
portions of cari-
at a etna 1 ler size.
but remain in
in the post-
Remain in grassy.
dean shrimp and
Growth is rapid in
general area
larval stage.
shallow water flats
then to penaeid
first year with
of nursery

until colder weather
lengths of 13 cm
grounds until

causes them to move

attained by the firat
cold weather

to deeper water.

winter and 25 cm
causes them to

their second winter. move to deeper


While tagging itudiea
how chat lone tea-
trout travel a( much
at 31} nilea, moat
atudiea ihow that
few fiih leave their
natal estuary.
C. nebulosua occu-
pies a more southern,
warmer water habitat
than doea C. regalia.
Liated aa the top
carnivore in noat
eatuarine communi-
ciea. Aa an adult,
will eat all other
fish of * smaller
aire aa well ai
ahrinp anJ lull
Longevity indicated
to be 8 to 9 yeara of
age. Generally macure
at one to three yeara
with 50X sexually
nature by end of
tecond year (25 cm
in length). All fiah
appeared to have
spawned by age three.
A 1978 report citea
the largest aeatrout
caught waa 16 pounda.
Hovemeat pat-
terns have
been traced to
the presence
or| absence of
penae id
Seasonal ooveaenia
correspond to water
temperature and
pawning aeaaon.
A top predator
which would be
in competition
with other pre-
datora such as
bluefish and
atriped basa.
both commercial
and recreational

Freshwater	Not applicable	Eggs need to be	Not applicable	Mo information
Eggs deposited in nests	aerated.
Egg	built near sand or
grsvel banks in still
or running water.
In freshwater, may	No information
move into tidal
Larvae water.
j*			;	;	;		:	
O No information	No information
Yolk sac larvae	No information	No information
bypass larval
stage, develop
directly to
juvenile stage.
Crowth continues	Remain in schools	No information
at 11 ppt salinity	until end of
or less.	first lunner;
initially guarded
by parents.
Haximuro salinity of	Omnivorous, soli-	Fish mature in one	Stay in waters	No information
l*i.5 ppt	t*ry, bottom feeder	to two years.	greater than 3 a.
Widespread in Bay.	-plant material	overwinter in
Adult	Prefer heavily silted	-email fish	Maximum length	deeper water (IS m),
bottom.	-clams and snails	61.0 cm.	move upstream to
Inhabit river channels	-worms	spawn in fresh*
and streams with slow	-insects	water,
current, ponds, and	-dead material	Males guard and
lakes.	aerate egg nasses.
Jones et al. 1978
Lippson et al. 1979
Daiber et al. 1976
Kendall and Schuart






F reahwate r
Not applicable
Eggs exposed to
Not applicable
information Jones et al.

Eggs deposited in

direct sunlight

nests in sand or

produce poor

gravel at depths of


Lippson t al
. 1979

several inches to

Eggs need to be

several feet.

ag i tated.

Daiber ct al.

No information
Yolk-sac larvae
Crouped inja

bypass larval
tight mass at

Found at bottom

stage, develop

directly to juvenile


Found among vegetation
No information
No information
Young juvenilea
informal ion

Juveni Ic
or other cover over

herded in schools

muddy bottoms.

by parents; may

remain in schools

throughout f irst


Adults are widespread
Omn ivorous t
Mature at 3 years.
A schooling bottom

throughout most of the
solitary bottom
Maximum length
species which is

Bay area, occurring in
(eede r
around 30.8 cm.
active primarily at

channels and shallow.
* plant material

night. Fish may

muddy water around
- etna 11 fish

burrow in soft sedi-

aquatic vegetation.
- claras and snaila

ments. Adults attend

Maximum salinity 10
- worms

eggs and orally

- insects


- dead material

Eggs 1 to 2 dayt old
Egg	tolerate salinity to
10 ppt; 3 day* and
older 16 ppt.
ro Juvenile
Not applicable
No information
, Not applicable
No information
Tolerate aalinitiea
up to 8 ppt.
Mo information
Abnormal develop-
ment occur1! at
temperacurea above
35C. Yolk-sac
larvae bypass larval
atage, develop to
juvenile stage.
Larvae guarded by
male first feu days
after hatching.
No information
Jones ct al. 1978
Lippson at al. 1979
Daibar t al. 1976
Tolerate salinities
up to 11-12 ppt.
Feed at surface
Crovth continues at Remain in schools
No information
11 ppt salinity or
up to several weeka.
Show strong schooling
and hiding tendencies
in first year.
Maximum salinity of
21.0 ppt, prefer leas
than 1.7 ppt.
Adult	Restricted distribution
in Bay.
- deeper channels of
lsrge rivers with
sluggish or swift
Omnivorous, soli-
tary, bottom
feede r
-	plant material
-	small fiah
-	clams and snail*
-	worms
-	insect*
-	dead material
Mature in 2 to 9
years. Haximum
length around
120.2 cm.
Hales construct nests
and guard eggs.
No informstion


Eggs are released over
Che continental shelf.
Not applicable
No information
Not applicable
Jellyfish, such as
the tea walnut
(Mnemiopsis leidyi),
predatory aarine
Hudson and Hardy 1974
Shea ct al. 1980
Lippson et al. 1979

Tolerate salinity 0-35
ppt. Optimum salinity
0-5 ppt in the estuary.
- planktonic cope-
No information
No information
Prey of predatory
fish and birds
Thomas 1971
Chao and Musick 1977
Peters and Kjelson
Tolerate salinity
0-34.2 ppt. Post-
larvae and young
fish concentrate at
salinities of 0.5-5.0
ppt; during years of
high population density
young may move into
freshwater. Prefer
muddy substrate.
Bottom feeder
-	benthic harp-
acticoid cope-
-	annelids
-	plant material
Crovth during
first summer is
rapid, juveniles
may measure 13 cm
by late fall.
Post-larvae are
carried into the Bay
. i '
in April through
enfcrsinment in botton
water*. School along
shpre during summer.
Young move downstream
! they grow.
Sas>e as above
6-34 ppt salinity.
Occur at depths' greater
than 1 m over soft
muddy bottom; larger
fish prefer channel
Bottom feeder
-	burrowing poly-
-	snnelids
-	sraalI crusta-
-	molluscs
-	mac rozooplankton
Reach sexual matu-
rity by the third
year; maximum
length around 33-35
Adults enter the Bay
in;ApriI and Hay,
leave for spawning
grounds offshore from
Aug. through Nov.
Prey of large game-
fish (atriped bass),
sharks, and the
target of recreational
and conmercial fish-

Tolerate 20-3} ppt
salinity, prefer 26.5-
27.5 ppt.
Not applicable
Salinity affects
egg development.
Eggs are carried on
currents in the Bay.
No information
Lippson 1973
Salinities greater than
17.5 ppt. Larvae are
pelagic, found in the
surface waters.
No information
Larval development
is affected by
salinity, tempera-
ture, turbidity,
and circulation
Larvae are initially
pelagic, but toward
the end of this
stage, they alternate
between a planktonic
and benthic exiatence.
Clan larvae are prey
of other filter
feeding organiams.
Shea et al. 1980
Castagna and Chanley
Optimum salinity 24-28
ppt, survive salinitiea
as low as 12.3 ppt.
Filter feeder
-	algae speciea
-	detritus
Crowth rates vary
with the type of
substrate used;
faster growth
occurs in coarser
aed iroents.
Young clams have bi-
sexual gonads,
usually dominated by
male characteriatica.
After the first
apawning season,
about 50Z of the juve-
niles become female.
Predatora include
-	oyster drills
-	blue crabs
-	moon snails
-	concha
-	horseshoe craba
-	sea stara
-	puffers
-	waterfowl

Salinities greater than
15 ppt. Hard clams
occur in subtidal
or intertidal waters
with solid substrate
(shell or rock).
Filter feeder
- algae species
Large clams measure
12-13 co in length.
Adults spawn during
neap tides; spawning
may be both thenaally
and chemically
-	cow nosed raya
-	drum fish
-	man

Eggs are released in
the ocean near the
Eggs	mouth of the Bay from
August through
Not applicable
No information
Not applicable
No information
Larvae, which enter the
Bay in fall remain in
channel waters at
depths greater than
3m; carried to the
salt water i-nterface.
No information
No informal ion
Larvae begin entering
the Bay in fall
through entrainaent
in bottom waters.
No information
Young juveniles are
found in channel waters
Juvenile of 0-21 ppt salinity.
Older fish tend to be
down-river from the
younger fish.
Juveniles less
than 10 cm
-	harpact icoid
Older juvenilea
-	polychaetes
-	crustaceans
-	fish
-	other inverte-
No growth occurs
during the winter
season; young fish
have been killed
during intensive
cold periods on
the nursery grounds.
Yearling croaker
leave in the fall.
Striped bass preda-
tion on overwintering
juvenilea may depress
the population;
juvenilea also preyed
on by bluefish.
Shea et al. I960
Hildebrsnd and
Schroedcr 1928
Lippson et al. 1979
Stickney et al. 197)
Chao and Musick 1977
Haven 19)7
Joseph 1972
Wallace 1940
Tolerate salinity	- small cruata-
0-40 ppt. Optimum ceans
Adult	salinity 10-34 ppt.	- annelids
Hard bottom at depths	- molluscs
greater than 3m.	- small fish
Croaker reach a
maximum length of
around )0 en.
Croaker enter the
Bay in spring,
remainingj in the
lower estuary until
fall, then they
migrate back to sea.
Water temperature
influences croaker
mi g rat ions.
Prey of top preda-
tory species (striped
bass and bluefish).
The target of a
commercial and recre-
ational fishery.

Tolerate salinity 0-6
ppt. Eggs are released
in tidal-fresh to low-
brackish waters in
shallows along the
Not applicable
Suspended sediment
levels about 1500
ppia increase incu-
bation period.
Not applicsble
No information
Tolerate salinity 0-8
ppt, prefer 0-1.5 ppt.
Larvae	Maximum depth 12 ft.
Larvae are found 'in
shallow water over
sand or gravel bars or
mud bottom.
-	rotifers
-	cladocerans
-	copepods
Temperature and
availab iIity of
rotifers affects
development of
yolk-aac larvae.
Remain in spawning
area, aettle to
bottom. General
downatream movement
aa larvae develop.
Compete with striped
bass larvae in
nursery areas.
Preyed upon by
fish (striped baaa)
and birds.
Tolerate sslinity 0-13
ppt, prefer 0-3 ppt.
Juvenile Found in shallow
sluggish water over
silt, mud, or vege-
tation; move to sandy
shoals and beaches at
-	copepods
-	cladocerana
-	inaect larvae
Crowth positively
correlated with
temperature and
solar radiation.
Crowth influenced
by population
Juveniles remain fn
nursery area at least
until 20 mm long, may
remain until 1 year
old. Juvenilea may
form large achools.
Tolerate salinity 0-30
ppt, prefer 4-18 ppt.
Adult	In summer, concentrate
near shoals, occasion-
ally in channel areas.
In winter, found in
deeper water; move to
channels during coldest
per iods.
Bottom oriented,
pise ivorous
-	smelt
-	yellow perch
-	young eels
-	young striped
-	insects
-	crustaceans
Crowth rates
decrease with age
and high population
density. Males
mature in 2 yeara,
females in 3.
Schooling adults
sre resident to the
Bay. White perch
are semi-anadromoua,
making spawning
migrationa upstream
in spring.
Shea et al. 1900
Lippsoo ct al. 1979
Hildebrand and
Schroeder 1928
Hudaon and Hardy 1974
Loos 1975
Mansueti 1961
Compete with striped
bass juveniles.
Preyed upon by fish
(striped bass, blue-
fish) and birds.
Preyed on by larger
fiah (atriped bass,
bluefish). Also the
target of a commercial
and recreational

Tolerate salinity 0-10
ppt. 1.5-3 ppC optinal.
1.0-2.0 a iec"'
optimum flow rate. Semi-
buoyant egg* released
in fresh to brackish
Not applicable
Salinity and temp-
erature influence
Not applicable
Prey of white perch.
Tolerate salinity 0-15
ppt. 5-10 ppt optimal.
0.3-1.0 m iec"'
optimal flow rate.
-	open waters
-	at 13 mra, move
inshore for first
Sight selective
-	copepods
-	rotifers
-	cladocerans
High prey concen-
trations necessary
for successful
first feeding.
Temperature and
adequate food
influence growth.
Positively photo-
trophic; newly-
hatched larvae sink
between swimming
efforts; at 2-3
days of age larvse
can swim continuously.
Compete with white
perch larvae in
nursery area.
Setiler et al. 1980
Boynton et al. 1981
Besven and Hihursky
Hoi 1 is 1952
Doroshev 1970
Shea et al. 1980
Hd. Dept. Nat. Res.
Juvenile ~
Juveniles 50-100 mm.
Tolerate salinity 0*33
ppt. Optimal 10-20
ppt. 0-1 m sec"*-
optinal flow rate.
- prefer sandy sub-
strate but found
over gravel bottoms
as well in shallow
Non-selec t ive
feede r
-	insect larvae
-	polychaetes
-	larval fish
-	aophipoda
-	nysids
Temperature and
population density
influence growth.
Downstream movement
of young-of-the-year
fish. Yearlings
school in rivers or
move into lower
eatuary in luoner.
Compete with white
perch in nursery
Prey of predatory
fish, birds, mammals
and man.
Tolerate 0-35 ppt
usually in salinities
greater than 12 ppt.
Summer habitat includes
high energy shorelines
with a current. Over-
winter in channels in
estuary or offshore
at depths below 6 n.
-	alewife
-	blueback herring
-	white perch
-	spot
-	menhaden
-	bay anchovy
-	croaker
Temperature, age,
population density,
and oxygen levels
influence growth.
Andromoua, migrate
to freshwater to
spawn, return to
lower eatuary or
ocean after spawning.
Young females (2-3
yr) migrate along
coast in summer with
older fish.
Compete with blue-
fish, weakfish, and
white perch. Com-
mercial and recre-
ational fishery for
striped bass.

Eggs are releaaed by
sedentary adults in
two spawning pesks,
spring and fall.
Not spplicsble
No information
Not applicsble
Ncf information

0-0.5 ppt salinity.
Non-tidal and tidal-
fresh water.
Not applicable
Low temperatures
during spawning
season cause an
extended incubation
pe r iod (2-3 wks);
larvae more devel-
oped at hatch than
other anadromoua
spec ie s.
Not applicable
No information
Settler et al. 1960
Lippson et al. 1979
Auld and Schubel 1974
Daiber at al. 1976
Huncy 1962

Tolerate salinity 0-2
ppt. Optimum 0-0.5 ppt
Shallow, freshwater;
survival reduced when
sediment concentrations
exceed 500 mg L~*.
- plankton
Salinities greater
than 2 ppt inter-
fere with larval
Larvae move down-
stream after
hatching; concentrate
near aurface, form
Preyed upon by white
perch, striped baas,
chain pickerel.

0.5-10 ppt, concentrate
at salinities of 5-7
ppt in summer. Found
in vegetsted areas near
-	small crusta-
-	insects
-	molluscs
Crows quickly
during f i rst year;
growth rate
decreases with age*
Females have greater
growth rate than
Initially concentrate
at surface, become
demersal at about 25
mm t
Preyed upon by fish
such as white perch
and striped bass,
birds, mammals.
Compete with white
perch and striped

Adu 1 C
Tolerate 0-13 ppt
salinity, prefer 5-7
ppt in summer. Prefer
higher salinity, tidsl
waters with muddy
-	bay anchovies
-	si1versides
-	minnows
-	isopods
-	araphipoda
-	anai1s
-	crustaceans'
Hales mature at 1
year of age,
females mature at
age 2 or 3; grow
to 53 cm. Large
populations cause
stunting of adults*
Spring migration
upstream to spawn;
return downstream
after spawning.
Competes with smaller
fish and invertebratea
for food. Preyed
upon by birds
(mergansers), fish
(gsrs and pikes), and


Eggs released off-shore Not applicable
in two diatinct wave a;
Egga spring spawning occurs
in the Culf Stream,
while aummer spawning
occura over the
continental shelf.
No information
Not applicable
Ho information
Lippaon et al. 1979
Hildebrand and
Schroeder 1928
Jonea at al. 1978
Daiber at al. 1976
No information
No information
No information
No information
Ho information
0-37.5 ppt aalinity.
The larger the juvenile
Juvenila population, the greater
the penetration into
the Bay.
-	copepoda
-	molluscs
-	pi ankt ivorous
-	any fish smaller
than themselvea
Juveniles grow
quickly during
the firatsummer.
Juvenilea from spring No information
spawning enter the
Bay in early summer;
leave the Bay by
late fall, heading
offshore and south-
7-36 ppt aalinity.
Both sexually mature
and immature adulta
Adult	enter the Bay; the
larger the adult
population, the greater
the penetration into
the Bay.
Voracious predator
-	menhaden
-	ailversides
-	bay anchovy
-	herring spp.
-	cruataceana
-	annelids
Bluefish are sex-
ually mature at
about 30.0 cm,
and reach a maximum
length of 93.4 cm.
Bluefish, a marine
apeciea, entera the
Bay in spring and
summer to feed.
Schoola of bluefiah
move aeaaonally in
relation to food
Compete with other
top predatora auch
aa atriped baas.
Target of a com-
mercial and recre-
ational fishery.

Compiled from Stevenson and Confer 1978.

Ceratophyllum demersum (Coontail)
Characea: Chara, Nitella, Toypel1 as
Elodea canadensis (Common el odea)
Myriophyllum spicatum (Eurasian watermilfoil)
Najas guadalupensis (Bushy pondweed)
Potamogeton pectinatus (Sago pondweed)
Potamogeton perfoliatus (Redhead grass)
Ruppia maritima (Widgeongrass)
Vallisneria americana (Wild celery)
Zannichellia palustris (Horned pondweed)
Zostera marina (Eelgrass)

Ceratophyllum demersum (Coontail)
Frequents quiet, freshwater pools and	Mason 1969
slow streams. Also 1n the Maryland
portion of the Chesapeake Bay.
Critical minimum temperature for	Wilkinson 1963
vegetative growth of 20C, with
optimum growth at 30C.
Essentially freshwater, but grows	Bourn 1932
normally in salinities under 6.50/00
Often grows independently of substrate	Sculthorpe 1967
Light, Depth and Turbidity
Shade tolerant, requiring a minimum of	Chapman et al. 1974
2 percent full sunlight for optimum
growth. Not considered to be depth
limited due to its rootless nature.
Turbidity is not as detrimental for
coontail as for rooted vegetation
because of shade tolerance and water
surface habitat.

Ceratophy 11 um demersum (Coontail)
Consumer Utilization
Foliage and seeds rated as having great	Sculthorpe 1967
importance to ducks, coots, geese, grebes,
swans, waders, shore and game birds.
Moderate importance as fish food, shade,
shelter and spawning medium.

(copied from Hotchkiss 1967)
Figure ! Coontail (CeratophyTlum demersum)

Characea: Chara, Mi tell a, Tolypellas
Primarily found 1n freshwater environments.	Hutchinson 1975
Some species inhabit brackish waters but	Cook et al. 1974
are not found in truly marine environments.
Found in temperate and tropical regions of
all the continents.
Germination of Characea occurs after main-	Hutchinson 1975
tenance at ,40C for one to three months.
Certain species ranged in salinities up to	Dawson 1966
15/oo with growth cessation and limited
survival at 20/oo.
Most species of Characea grow in silt or	Hutchinson 1975
mud substrate though a small number of
species tend to grow in shallow water on
sandy bottoms.
Light, Depth and Turbidity
The Characea are capable of surviving in	Hutchinson 1975
low light intensities. Have been found
inhabiting fresh water at depths up. to
65.5 m (Lake Tahoe), with incident

Characea: Chara, Nitella, Tolypellas
Conti nued
radiation of slightly more than 2 percent
of that reaching the lake surface.
Consumer Utilization
Consumed by many kinds of ducks, especially Martin and Uhler 1939
diving ducks. Also provides habitat for
aquatic fauna.

(copied from Hotchkiss 1967.)
Figure 2. Muskgrass (Chara sp.)

El odea canadensis (Common el odea)
Endemic to North America and naturalized
to many industrialized nations of Europe
and the southern hemisphere.
Water temperatures of 15 to 18C are
necessary for successful growth.
Yeo 1965b
Sal inity
Salinity range of fresh water to brackish
water of 10/oo.
U.S. Army Corps of
Engineers 1974
Prefers a soil to sand substrate. Grows
better when rooted than when suspended.
Yeo 1965b
Hutchinson 1975
Light, Depth and Turbidity
Maximum frequency of el odea is between
3.0 m and 7.5 m depth. Capable of
quickly growing up-through covering
layers of silt.
Hutchinson 1975

El odea canadensis (Common elodea)
Consumer Utilization
Has little value to water fowl. Generally	Martin and Uhler 1939
unpalatable to aquatic insects. Epiphytes	Hutchinson 1975
grow abundantly between the teeth on the
leaf margins and on the upper leaf surfaces.

(copied from Hotchkiss 1967)
Figure 3. Common elodea (Elodea canadensis)

Myriophyllum spicatum (Eurasian watermilfoil)
Di stribution
Native to Europe and Asia, is widespread
in Europe, Asia and parts of Africa.
Found in Chesapeake Bay area, also infested
many lakes in New York, New Jersey and
Anonymous 1976
Springer 1959
Springer et al. 1961
Stotts 1961
Found growing in temperatures ranging from
0.1 to 30C.
Anderson 1964
Anderson et al. 1965
Found in salinities ranging from 0 to
20/oo. Grows best in salinities of
0 to 5 /.' Inhibition starts at 10/
and becomes severe from 15 to 20/Oo.
Rawls 1964-
Boyer 1960
Grows best in soft muck or sandy muck
bottoms. Maximum density coincides with
fine organic ooze while minimum density
is found in sand.
Patten 1956
Anderson 1972
Steenis et al . 1967
Philipp and Brown 1965
Springer 1959
Light, Depth and Turbidity
Sensitive to turbidity and grows in water
more than 2 m deep, if clear. Limited to
1.5 m in extremely turbid waters.
Southwick 1972
Titus et al. 1975.

Myriophyllum spicatum (Eurasian watermilfoil)
Conti nued
Consumer Utilization
Florschutz 1973
Martin et al. 1951
Springer 1959
Springer et al. 1961
aufwuchs which later become food for higher
life forms. Crowds out more desirable
Low grade duck food. Found in digestive
tracts of 27 Canada Geese, 6 species of
dabbling ducks, 4 species of divers and
31 coots in the vicinity of Back Bay and
Currituck Sound. Offers support for

(copied from Hotchkiss 1967)
Figure 4- Eurasian water-milfoil (MyriopMTium;

Najas guadalupenses (Bushy pondweed)
Essentially freshwater or brackish water	Hotchkiss 1967
species, ranging from Oregon to Quebec,	Martin and Uhler 1939
and California to Florida.
No information
Prefers 3/0o salinity. Found in Potomac	Steenis 1970
River at salinities of 6 to 9/oo.
Prefers soils containing a predominance of	USDI 1944
sand, but tolerates substrate of pure muck. Martin and Uhler 1939
Light, Depth and Turbidity
Usually found in depths ranging from 0.3 to Martin and Uhler 1939
1.2 m, but has been recorded at depths over
6 m.
Consumer Utilization
Excellent in food value for waterfowl. Birds Martin and Uhler 1939
eat both the seeds and the leafy plant parts.

(redrawn after Hotchkiss 1967)
Figure 5. Naiad (Najas sp.)

Potamogeton pectinatus (Sago pondweed)
Oi stributlon
Range includes freshwater streams and	Martin and Uhler 1939
ponds, also brackish coastal waters of	Hodgeson and Otto 1963
the United States and portions of Canada.	Devlin 1973
Most abundant in the northwestern states
and the Chesapeake Bay in the United States.
Reported to be a pest species of irrigation
systems in the west, and in cranberry bogs
of Massachusetts.
Germination shown to.occur when water	Yeo 1965b
temperature reaches 15 to 18C.
Sal i n'ity
Maximum seed production, seed germination	Teeter 1965
and vegetative growth occurs in freshwater.
Salinities of 8 to 98/0o generally decreased
growth and germination rates by 50 percent.
Grows on both mud and sand bottoms. Prefers Sculthorpe 1967
silty bottoms.	Rickett 1923
Light, Depth and Turbidity
Requires at least 3.5 percent total sunlight Bourn 1932
for growth. Shading produces yellowed,
sparse foliage, elongated nodes and rigid
unbranched stems.	r.ifi

Potamogeton pectinatus (Sago pondweed)
Conti nued
Consumer Utilization
One of the more Important waterfowl plant	Martin and Uhler 1939
foods. Nutlets and tubers reported to be	Fassett 1960
excellent food source for ducks; rootstocks
and stems are consumed to a lesser degree.
Also provides protective habitat for fish,
oysters, and benthic creatures.

(copied from Hotchkiss 1967)
Figure 6. Sago pondweed (Potamoqeton pectinatus)

Potamogeton perfoliatus (Redhead grass)
Fresh and moderately brackish waters,.
It has been found in Labrador, Quebec,
New Brunswick and extends to Eurasia,
northern Africa and Australia. Its
presence has been recorded in the
Chesapeake Bay through 1976.
Experiments showed that respiration and	Anderson 1969
Og consumption increased as temperatures.
increased from 25 to 408C, with death
occurring at 45C.
1.5 to 19/oo, tolerant to 25/0o.	Anderson 1969
Grows best on a mixture of organic material Misra 1938
and silt with a minimum carbon to nitrogen
ratio, a high capacity to recycle ammonia
and a low redox potential. Moderately
organic muds fairly rich in nitrogen and
exchangeable calcium are more suitable
than highly organic muds.
Ogden 1943
USFWS Migratory Bird and
Habitat Research
Laboratory 1976

Potamogeton perfoliatus (Redhead grass)
Light, Depth and Turbidity
Usually found 1n still or standing water
ranging from 0.6 to 1.5 m depth. Maximum
rate of photosynthesis attained where
Hght Intensity was about 1.1 g cal/cm .
Consumer Utilization
Seeds, rootstocks and portions of the stem	Martin and Uhler 1939
are consumed by Black Ducks, Canvasbacks,	Fassett 1960
Redheads, Ringnecks and other duck species.
Also eaten by geese, swans, beaver, deer,
muskrat. Provides protective cover for
various aquatic organisms.
Felfoldy 1960
Martin and Uhler 1939

(copied from Hotchkiss 1967)
Figure 7. Redhead grass (Potamogeton perfoliatus)

Ruppia maritima (Widgeongrass)
Inhabits a wide range of shallow, brackish
pools, rivers and estuaries along the
Atlantic, Gulf and Pacific Coasts. Also
occurs in fresh portions of estuaries,
alkaline lakes, ponds and streams and in
shallow, saline ponds and river deltas of
the Great Salt Lake region.
Martin et al. 1951
Radford et al. 1964
Ungar 1974
Chrysler et al. 1910
j*. maritima appeared to have two growing
Joanen and Glasgow 1965
seasons within the temperature range of.
18 to 30C. Growth ceased outside this
range although some fruiting and flowering
occurred at temperatures higher than 30C.
Tolerant of a broad salinity range, from	Steenis 1970
5.0 to 40.0/oo. Tension zone of over	Anderson 1972
30/oo. Flowering and seed set occurs	McMillan 1974
in range of tapwater to 28/0o.
Prefers soft bottom muds or sand. Has been Anderson 1972
found growing on shallow sand shell gravel	Zenkevitch 1963
soils in Russian rivers and streams.

Ruppia maritima (Widgeongrass)
Light, Depth and Turbidity
Optimum production in laboratory studies	Joanen and Glasgow i965
occurred at depth of 60 cm. Is found at
depths of a few inches to several feet.
Turbidity tolerance less than 25-35 ppm in
small ponds; turbidity is especially harm-
ful to young plants prior to the stems
reaching the surface.
Consumer Utilization
Serves as food for numerous species of
ducks, coots, geese, grebes, swans, marsh
and shore birds of the Atlantic, Pacific
and Gulf Coasts. Also used as nursery
grounds and as a fish spawning medium and
cover for marine organisms.
S'culthorpe 1967
Martin and Uhler 1939
Kerwin 1975b

(copied from Hotchkiss 1976)
Figure 8. Widgeongrass (Ruppia maritima)

Vallisneria americana (Wildcelery)
Freshwater macrophyte occurring in the	Martin and Uhler 1939
tidal streams of the Atlantic Coastal
Grows best in temperature range of 33 to	Wilkinson 1963
36C. Arrested growth occurs below 19C.
Laboratory tests showed that Val1isneria	Bourn 1934
could not be maintained in salinities
greater than 4.2/0o.
Grows equally well in sandy soil and mud.	Schuette and Alder 1927
Hutchinson (1975) found that V_. americana	Hutchinson 1975
thrived.best in a soil of 6.5 percent
organics, 8.78 percent gravel, 21.46
percent sand, 47.90 percent silt, 14.26
percent clay.
Light, Depth and Turbidity
Able to tolerate muddy, roiled water.	Steenis 1970
Usually found in shallow water (0.5 to
1.0 m).

Val1isneria americana (Wildcelery)
Consumer Utilization
All parts of the plant structure are	Sculthorpe 1967
consumed by fish, ducks, coots, geese,
grebes, swans, waders, shore and game
birds. Also serves as a shade, shelter
and spawning medium for fish.

(copied from Hotchklss 1967)
Figure Wlldcelery (ValHsneria americana)

Zannichellia palustris (Horned pondweed)
This species has been documented in every	Deane 1910
state in continental United States; however, Fassett 1960
it is not a conmonly occurring submerged
aquatic. Reported occasionally in brackish
marshes along the New England coast, rarely
found inland. Recorded in Chesapeake Bay
and south to Currituck and Pamlico Sound
area, North Carolina.
In the Chesapeake Bay, the Zannichel1ia	Tutin 1940
populations decline rapidly when tempera-
tures reach 30C. Reported to exist in
temperatures as low as 10.5 to 14.8C.
Tolerates freshwater, but prefers brackish	Radford et al. 1964
waters to 20%o.
Tends to grow in clay to sandy sediments.
Light, Depth and Turbidity
Prefers shallower water than other submerged Correll et al. 1977
aquatics. May need higher light intensities
than others; good growth obtained at 4 to 7
percent of the maximum noon summer sunlight.

Zannichellia palustris (Horned pondweed)
Consumer Utilization
Fruits and sometimes foliage are
waterfowl in brackish pools.
good for	Fassett 1960

(copied from Hotchkiss 1967)
Figure 10- Horned pondweed (ZannicheTlia palustris)

Zostera marina (Eelgrass)
On the Pacific Coast of North America,
eelgrass extends from Grantly Harbor,
Alaska, to Agiahampo Lagoon in the Gulf
of California. On the Atlantic Coast of
North America, eelgrass extends from
Hudson Bay, Canada, the southern tip of
Greenland, and one locality in Iceland,
to Bogue Sound, North Carolina.
McRoy 1968
Steinbeck and Picketts
Cottam 19341)
Ostenfeld 1918
Phillips 1974a
Tolerate temperatures from'-6C to 35C.
Photosynthesis decreased sharply above
35C. Death occurred after exposure to
Biebel and McRoy 1971
Can tolerate salinities ranging from
8/0o to full strength seawater (35/oo).
Phillips 1974a
Arasaki 1950a,, 1950Jb
Martin and Uhler 1939
Found growing on a wide variety of sub-
strates, from pure firm sand to pure firm
Phillips 1974a

Zostera marina (Eelgrass)
Light, Depth and Turbidity
Has been found growing from about 2 m above Cottam and Munro 1954
MLW (minimum low water) to depths down to	Phillips 1974a_
30 m. Low light intensity conditions	Backman and Barilotti 1976
inhibit flowering and turion (young branch)
density is decreased in shaded plots.
Consumer Utilization
The only groups of animals that consume	Cottam 1934Jd
eelgrass directly are waterfowl and sea	.Addy and Aylward 1944
turtles. Eelgrass beds provide important	Gutsell 1930
habitats and nursery areas for many forms
of invertebrates and vertebrates, which
then serve as food sources of species at
higher levels.

(copied from Hotchkiss 1967)
Figure 11. Eelgrass (Zostera marmaji

Environmental Requirements of certain fish in Gulf of	estuaries
Anchoa hepsetus (striped anchovy)
Anchoa mitchi111 (bay anchovy)
Arius felis (sea catfish)
Paralichthys lethosigma (southern flounder)
Mugil cephalus (striped mullet)
Pomatomus saltatrix (bluefish)
Poqonias cromis (black drum)
Sciaenops ocellatus (red drum)
from. Benson 1982

Anchoa hepsetus (striped anchovy)
The distribution of all 1 i fe" stages. of str.i ped anchovy appears to be
limited primarily by salinity. Christmas and Waller (1973) reported this
species in salinities ranging from 5:0 ppt to 3.5 ppt. Perry and Boyes
(1978) collected 95.6% of their specimens in salinities between 20 and 30
ppt, largely in waters south of the Gulf Intracoastal Waterway. This fish
is most abundant at temperatures ranging from 20 to 30C (68 to 86F)
(Perry and Boyes 1978).
Anchoa mitchilli (bay anchovy)
Although the distribution of the bay anchovy in Mississippi Sound waters is
not greatly affected by differences in salinities, low winter temperatures
appear to cause -some movement to deeper, warmer offshore waters (Springer
and Woodburn 1960; Christmas and Waller 1973). Swingle (1971) found them
to be nearly equally distributed in salinities between 5 and 19 ppt in
Alabama coastal waters. Highest catches were in salinities ranging from
20.0 to 29.9 ppt. In Mississippi Sound, Christmas and Waller (1973)
established no relationships between the distribution of anchovies and
salinities above 2 ppt. Perry and Christmas (1973) found larvae in
Mississippi waters in salinities ranging from 16.6 to 27.8 ppt. Bay
anchovies were taken at temperatures from 5.0 to 34.9C (41.0 to 94.8F),
but the largest numbers were in water temperatures between 10.0 and 14.9C
(50.0 and 58.8F) (Christmas and Waller 1973).
Arius felis (sea catfish)
Sea catfish in estuaries in the summer are most abundant in.;water
temperatures from 19 to 25C (66 to 77F). Year round, they have been
taken in the range of 5.0 to 34.9C (41.0 to 94.8F) (Perret-et al. 1971;
Adkins and Bowman 1976; Drummond and Pellegrin 1977; Johnson 1978); This
euryhaline species is common in "salinities from 0 to 45 pp.t, but some
tolerate 60 ppt. A preference of higher salinities has been suggested
(Gunter 1947; Johnson 1978; Lee et al. 1980). Breeding occurs in waters
having a salinity range of 13 to 30 ppt.
,The developmental stage of larvae incubating in the oral cavity may
determine the location of the parent, male (Harvey 1971). ; Younger larvae
tolerate salinities up to 12.8 ppt, . but: more developed larvae tolerate
salinities of 16.7 to 28.3 ppt (Harvey 1971). Juveniles are most numerous
in low salinities (Johnson 1978).
Although minimum dissolved oxygen requirements of sea catfish are not
known, this fish sometimes lives in dredged semiclosed and closed canals
that are characterized by low oxygen concentrations (Adkins and Bowman
1976). They are found in moderately turbid water (Gunter 1947; Lee et al.
Sea catfish principally live at depths from 4 to 7 m (13 to 23 ft), but may
occupy waters as deep as 36 m (118 ft) (Lee 1937; Johnson 1978). Major
substrates are muddy or sandy bottoms rich in nutrients (Etchevers 1978;
Shi pp 1981).

ParaHchthys lethostigma (southern flounder)
The southern flounder 1s euryhaline, occurring in waters with salinities
from 0 to 60 ppt. The normal range is from about 10 to 31 ppt. They live
at water temperatures from 9.9 to 30.5C-'(49.8 to 86.9F), but are most
common between 14.59; and 21.6C .(-.58.1" and 70.9F) (Stokes 1973). The
temperatures and salinities where" southern flounder were collected in
Mississippi Sound by Christmas and:Waller (1973) ranged from 5.0 to 34.9C
(41.0 to 94.8F) and 0.0 to 29.9 ppt.< The juveniles may live in fresh-
water for short periods.
Juveniles are usually most abundant in shallow areas with aquatic
vegetation (shoal grass and other sea grasses) on a muddy bottom. Adults
also tend to favor aquatic vegetation such as Spartina alterniflora. Some
flounders overwinter in the deeper holes and channels of estuaries, but
most (adults and second-year juveniles) migrate to Gulf waters in the fall
(Gunter 1945).
Mugil cephalus (striped mullet)
Striped mullet live in freshwater and in salinities up to 75 ppt. In Texas
estuaries the mullet were about equally distributed in water of all salin-
ities- (Gunter 1945). They have been taken in Mississippi in salinities
ranging from 0.0 to 35.5 ppt (Christmas and Waller 1973).
Fish less than 3.6 cm (1.4 inches) long are most abundant in salinities
from 0.0 to 14.9 ppt. Juveniles (up to 7.9 cm or 3.1 inches long) prefer
lower salinities and warmer waters than larger fish. Juveniles are mostly
taken in salinities from 0 to 10 ppt when temperatures range from 25 to
30C (77 to 86F). Fish up to 11 cm (4 inches) long are abundant at
salinities from 0 to 20 ppt at temperatures of 7 to 30C (45 to 86F)
(Etzold and Christmas 1979)."' Highest catches in samples from Mississippi
Sound were in the range of 7 to 20C (45 to 68F). Mullet are often
killed in water temperatures less thafl 5C (41F) (J.C. Parker 1971), and
they tend to aggregate in sheltered areas before the arrival of cold
Pomatomus saltatrlx (bluefish)
Temperature and salinity are'the only" factors cited by Wilk (1977) as
determinants of the distribution of bluefish on the Atlantic coast.
Extensive data from egg and larval rcollections on the outer continental
shelf of Virginia showed that maximum;"spawning occurred at 25.6C (78.1F)
with none below 18C (64F) (Norcross et al. 1974). 'Minimum spawning
temperature 1s about 14C (57F) (Hardy 1978). Bluefish seem to prefer
salinities from 26.6 to 34.9 ppt. Limited larvae collections in:the Gulf
of Mexico were found in a temperature range of 23.2 to 26.4C (73.8 to
79.6F) and a surface salinity range of 35.7 -to 36.6 ppt (Barger et al.
1978). In estciaries they rarely live in salinities below 10 ppt. Hardy
(1978) suggested 7 ppt as the minimum salinity. Lacking are data on the
effects of substrate, turbidity, tides, or dissolved oxygen on bluefish
distribution. Bluefish activity patterns are highly oriented to vision
(011a and Studholme 1979), however, and bluefish are not likely to frequent
turbid areas.

Pogom'as cromis (black drum)
Black drum are euryhaline during all life stages, i.e., they occur in
salinities from 0 to 35 ppt. The species is most common at salinities
ranging from 9 to 26 ppt (Gunter 1956; Etzold and Christmas 1979), but some
inhabit water with salinities as high as 80 ppt. The black drum is usually
taken at water temperatures from 12 to 30C (54 to 86F). This fish
inhabits areas with sand or soft bottoms as well as brackish marshes and
oyster reefs (Etzold and Christmas 1979). The preferred habitat of
juveniles during the first 3 months are muddy, nutrient-rich, marsh
habitats such as tidal creeks.
Sciaenops ocellatus (red drum)
The general salinity range for red drum is 0 to 30 ppt, but some tolerate
salinities up to 50 ppt (Theiling and Loyacano 1976). Larvae and juveniles
were taken at salinities between 5.0 and 35.5 ppt in one study (Christmas
and Waller 1973), but most occur at salinities from 9 to 26 ppt. The
larger fish seem to prefer higher salinities. Red drum are most abundant
in salinities from 20 to 25 ppt (Etzold and Christinas 1979), and from 25 to
30 ppt (Kilby 1955). Overall, red drum prefer moderate to" high salinities.
Red drum have been observed in water temperatures ranging from 2 to 29C
(36 to 84F). Some young fish were found in a temperature range of 20.5
to 31C (68.9 to 87.8F). The highest catches were at temperatures
between 20 and 25C (68 and 77F) (Etzold and Christmas 1979). Large
numbers of red drum have been reported killed in severe cold spells (Adkins
et al. 1979).
Red drum thrive in waters over sand, mud, or sandy mud bottoms and
occasionally in and among aquatic vegetation.