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- U.S. EPA
513 569 756S
P. OS
IgJVUD
MIDDLE SNAKE RIVER
WATERSHED
Ecological Risk Assessment
Planning and Problem
Formulation
RISK ASSESSMENT FORUM
U. S. ENVIRONMENTAL PROTECTION AGENCY
•." > DRAFT, June 17,1996
025
x. -
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ACKNOWLEDGMENTS
This risk assessment was prepared by a diverse team representing organizations and. agencies
interested in management and protection of the biota of the Middle Snake River watershed. The risk
assessment was sponsored by the U.S. Environmental Protection Agency's Office,of Water and Office
of Research and Development under a Risk Assessment Forum Technical Panel. Dr. Jeroen Gerritsen
•of Teu-a Tech, Inc. provided .technical assistance to the team. The conclusions and recommendations
presented herein are those of the Middle Snake River "Watershed Ecological Risk Assessment Team.
• ~ , •.•.., /
TECHNICAL PANEL CHAIR:
Suzanne Marcy, U.S. EPA, Office of Research and Development
TEAM CO-CHAIRS:
Pat Cirone, U.S. EPA, Region 10, Seattle, Washington ,
Jerry Filbin, U.S. EPA, Office of Policy, Planning and Evaluation, Washington, D.C.
TEAM MEMBERS:
John Yearsley, U.S. EPA, Region.10, Seattle, Washington
DRAFT-Jwm 17. 1996
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Middle Snake River Watershed Ecological Risk Assessment
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TABLE OF CONTENTS
Acknowledgments '............... .'. •.-..'. :......' i
Table of Contents ; '.''. . Hi
List of Figures and Tables ,...'..... iv
Executive Summary v
Introduction . . l
1.0 Planning '...-...- '..' ...'..,....... 5
1.1 Public, Private, and Governmental Groups Active in the Mid-Snake River Watersheds
1.2 Planning Process • • • ...... '.•• : 5
1.3 Management Concerns and Goals for the Ecological Risk Assessment . '. . 6
1.4 Scope, Complexity and Focus of the Ecological Risk Assessment .7
2.0 Assessment of Available Information ........ .... . , 9
2.1 Characterization of the Ecosystem at Risk 9
2. . 1 Demographics . * . . ,.....;...• 9
2. .2 Land Use 9
2. .3 Meteorology . ; 13
2. .4 Geology 13
2, .5 Hydrology . ............ . . ...... . 13
' 2. .6 Fish .,;...,...'.;....'..'.;..; . . . . 14
. 2. .7 Invertebrates ."..' .15
2.1.8 Vascular Macrophytes and Algae ...;... 16
2.1.9 Wetland and Riparian Vegetation and Waterfowl ; ...... 16
2.2 Ecological Effects Observed in the Watershed ; . . 17
2.3 Stressors . .... .... 19
2.3.1 Sources of Stressors .................,:...... 19
2.3.2 Stressor Characteristics 20
2.3.3 Secondary Stressors . . . . 26
3.0 Assessment Endpoints . . . . . . '. . . .'.. 29
4.0 Analysis Plan 31
4.1 Assumptions 31
4.2 Conceptual Model . . ....-.'. , ...:.... 31
4.3 Measures of Exposure and Effect . . .• . . 32
4.4 Simulation Modeling ......... ,,'. .> . -.....' 33
5.0
References .... 41
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Table of Contents (continued) .
Appendix A Participants in the Protection of the Middle Snake River 44
Appendix B Regulatory and Non Regulatory Framework • • • • .•'... 45
Appendix C Ecological Components of the Middle Snake River . 51
LIST OF FIGURES
1. • Water quality control and management, Snake River Basin, 1968 2
2. , ' Map of Mid-Snake River watershed from the USGS hydrologic unit '. .... 3
3. Schematic diagram of the Mid-Snake River watershed 10
4. Map of Idaho showing Snake River and Mid-Snake River study
area (highlighted) • • • 11
5. Land management, Snake River, Idaho from Idaho Department of Water
Resources, 1986 . . 12
6. Conceptual diagram of the river continuum of alternating lotic and lentic habitats 18
7. A conceptual water quality model of the Middle Snake River .:."..... 35
8. Conceptual model describing interactions of stressor and the effects on cold
water fishery in the Mid-Snake River ........:... 36
9a. Protection of endangered and other ecologically important benthic invertebrate
species (sediments) 37
9b. Protection of endangered and other ecologically important benthic invertebrate
species (nutrients) 3°
10. Conceptual model for vascular macrophyte growth as applied to the
Mid-Snake River 39
11. Conceptualization of risk outcome as applied to the development of a
Total Maximum Daily Load for total phosphorus 40
LIST OF TABLES
1. Primary Anthropogenic Stressors on the Snake River Between Milner Dam
and King Hill, Idaho 20
2. Stressor Sources and Characterization in the Mid-Snake River 21
Middle Siiake River Watershed Ecological Risk Assessment
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EXECUTIVE SUMMARY
- " ' / . *
The Snake River Watershed
The Snake River is the tenth longest river in the United States. Prior to the 1960s, it was the most
important drainage in the Columbia River system for the production of native anadromous fishes
including salmon, trout, and sturgeon. The Snake River extends 1,667 kilometers from its origins in
western Wyoming to its union with the Columbia River at Pasco, Washington. Its watershed
encompasses an area of approximately 267,000 square kilometers (km2) in Idaho, Oregon, Wyoming,
Nevada, Utah, and Washington. The river reach of concern, hereafter referred to as the Mid-Snake
River, spanning roughly 100 km-, lies in the west-central Snake River Plain of southern Idaho (Figure
4). The contributing watershed includes 22,326 square km2 of land below the Milner Dam and "
adjacent to the study reach. Beneath the Snake River Plain is the largest and most productive aquifer
in the Northwest, which supplies most local municipal water systems • , •
As a result of human activities spanning the past century, water quality and biological resource
problems have developed in the Mid-Snake River and its tributaries. The rapid rate of human
population growth projected for the southern Idaho region, as well as an increasing demand for
energy, irrigation resources, springs, and dairy feedlots, place additional burdens on an ecosystem that
already has been substantially changed by human activity during this century. T^his ecological risk
assessment, one of five EPA case studies, was undertaken to address such concerns by analyzing the
Mid-Snake River'sstressors and resulting ecological effects and to stimulate broader public awareness
and participation in decision-making for reducing ecologicalrisks.
Historically, this portion of the Snake River has been valued as a source of water for irrigation, for the
generation of hydroelectric power, and for the production of fish in commercial hatcheries. Water
quality and quantity have historically supported native benthic and pelagic biota requiring cold, swiftly
flowing water that is low in sediment, including migrating salmonids and other fish species, as well as
invertebrates.
The demands on the water resources have transformed this once free-flowing river segment to one
with multiple impoundments, flow-diversions, and increased chemical and microbiological pollutant
loadings. Physical changes include significant alterations to rapids and pool areas of the river.
Resulting biological changes include loss of native macroinvertebrate species, an invasion and.
dominance of exotic species', an.expansion of pollution-tolerant organisms, and excessive growth of
macrophytes and algae. Reducing and mitigating impacts to the watershed cannot return the Mid-
Snake River to its original state, but they can provide a better environment for the natural heritage
resources which have • .
Management Goals '•'„.''
Several agencies and organizations have been identified as active in decision making and management
activities for the Mid-Snake River—including federal state, county, and private organizations,
academic researchers, and interested .citizens. The perspective .with which local, state, and federal
planning agencies, scientists, and the general'public view this watershed is changing as the community
becomes more aware of the impacts of the activities in the watershed on the ecology of the river. '-
DRAFT-June 17, 1996
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This risk assessment was designed with several long term goals in mind: .
>• Develop an ecosystem perspective for environmental planning that can he used in
other river basins throughout the region.
> Increase the knowledge of the and function of the Mid-Snake River ecosystem.
>• Expand the scope of our simulation methods to include more complex compartments
in the ecosystem. ; •
A series of management subgoals, were developed for this risk assessment in order to move the
process toward attainment of the long term goals. The general management goals for this project
Include several specific objectives: ,
•• Attainment of State Water Quality Standards
»• Designation as a protected area
' »• Sustained economic activity in the region . .
>• Water for hydropower . ,
»• Water for irrigation needs .. •
>• Conservatipn of wildlife and game species
> , Recovery of endangered species • .
>• Recreational uses
The short-term objectives for this project are associated with, and largely driven by, the specific
requirements of state and federal environmental legislation and the development of comprehensive
land-use plans at the county level: • •
•• The establishment of total maximum daily loadings for water quality limited segments
of the river.
•• The review of permits for licensing existing and proposed hydroelectric projects
•• The evaluation of management plans for identification and control of nonpoint source
pollution ' ' ' -
»• Assisting in the writing of permits for National Pollution Discharge Elimination
System •. .
v; . Middle Snake River Watershed Ecological Risk Assessment
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Assessment Endpoints
Three assessment endpoints were selected for the Mid-Snake River risk analysis:
> Reproduction and recruitment of cold water fish, such as trout and sturgeon.
.*' Reproduction and recruitment of threatened and endangered macroinvertebrates.
»• Extent of open water free from macrophytes. •
The three assessment endpoints are related to several of the management subgoals. Coldwater fish; in
addition to being valuable sport fish, are top predators of the river ecosystem. In addition to the
restoration of invertebrate and fish species, the reduction in vascular macrophyte biomass is essential
to assure the restoration of cold water biota. .•-..,
Conceptual Model .
Conceptual model development requires an evaluation of the ecological resources of value (assessment
endpoints), the stressors affecting them, and the interactive relationships between resources and
stressor effects. The conceptual model for this ecological risk assessment of the Mid-Snake River '
watershed incorporates the descriptions of the ecological components, stressors, ecological effects, and
exposure scenarios to assist in developing hypotheses regarding how each stressor may affect the
watershed. . , - . -
1 , . ' ' - " • ' t
Prior to the development of hydropower on the Snake River, the Mid-Snake was host to a variety of
anadromous fish species extending up to Shoshone Falls, which acted as a natural barrier for Snake
River fish and fauna. The anadromous salmohids were first severely impacted .by the construction of
Swan Falls Dam. Several major hydroelectric events severely impaired, and finally terminated,
lamprey, salmon and steelhead migration into the Mid-Snake area. The Snake River runs of fall
chinook salmon and spring/summer chinook salmon were listed as endangered in 1994. According to
the US Fish and Wildlife Service draft Recovery Plan,, remedial actions to protect fish and wildlife
endangered snails in the Mid-Snake may also benefit the recovery of these fish stocks in the lower
Columbia River.
! ' '. ' L '" ' '
The historic diversity of molluscs in the Snake River won exceptionally high for western North
America. Most cold-water native molluscs now survive only in limited spring fed areas in.the Mid-
Snake River. Several Snake River invertebrates are listed as threatened, endangered, extinct or
candidate. Several of these species—including the Banbury Springs limpet, Snake River Physa, the
Bliss Rapids snail, and the Idaho Spring snail—are found nowhere else outside of the Mid-Snake River.
Currently, vascular macrophytes cover up to 40% of the benthic habitat in some reaches of the Mid-
Snake. The dominant species, Ceratophyllum demersum and Potamogeton pectinatus 1979 are
generally associated with well buffered, nutrient rich waters. Blooms of planktonic, periphytic, and
epiphytic algae, occur continuously during the spring and summer.
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Three primary stressors have been identified for this risk assessment: flow alteration, sediment
loading, and nutrient loading. Although there are many other physical, chemical, and biotogical
stressors in the watershed, the hypothesis is that their importance will be minimized or eliminated if
the key primary stressors are removed. Sources of stressors are directly and indirectly related to land
use activities within the contributing watershed and from hydrologic modifications to the river segment
of concern. Each of the primary stressors has a profound impact on the assessment endpoint resources
(fish, invertebrates, and macrophytes). •
Flow Alteration
Flow alterations in the Mid-Snake River result from multiple impoundments and flow.modifications in •
the mainstem, tributaries, and ground-water outfalls. Consequently numerous hydroelectric facilities
are located in this area. Flow alteration, resulting in both periodic increases and/or decreases in the
usual supply of fresh water to a river, include diversions, withdrawals, and impoundments (USEPA,
1993): The results of flow alterations, such as those on the Mid-Snake River, contribute to many
sources of nonpoint pollution, including:
•• Changes in the timing and quantity of freshwater inputs downstream;
>• Reduced downstream flushing; . - ,- _'
»• Sediment deposition-rsiltation of gravel bars and riffle complexes;
t '
»• Erosion of the streambed and scouring in tailwater reaches;
>• Increased deposition in areas of low water velocity resulting in formation of vascular
macrophyte beds and loss of fish spawning habitat;
*• Increased downstream temperature;
»• Reduced downstream dissolved oxygen; and
•• Velocity changes. .
Since there is considerable competition among the various users for water withdrawal rights, the
ecological integrity of the Mid-Snake River ecosystem is severely stressed by reductions in flow. This
is a particularly acute problem in.the spring and summer months because of irrigation diversions which
remove a considerable volume of water from the Mid-Snake River.
The dynamics of flow influences the process of sediment suspension and deposition. Altered flows
change the pattern of sediment scouring and deposition by reducing downstream flushing and increase
the siltation of gravel bars and riffle complexes. Clear water released from dams results in increased
erosion of the riverbed and bank scouring occurs below dams, particularly in the littoral shoreline
areas. These habitats are most often altered in ways that are not compatible with the survival of
benthic communities. , .
Middle Snake River Watershed Ecological Risk Assessment
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Sediment Loading
Sediment has direct ecological effects on macroinvertebrates by blanketing important habitat and
smothering species that depend upon aerobic sediments. Fine sediments may clog the gills or feedine
apparatus of species adapted for living in coarser .sediments and'is not functional as a spawning
substrate for most species. Sediment deposition may promote vascular macrophyte growth alter the
underlying sediments, and make them unsuitable for indigenous macroinvertebrates. Sediment in
suspension may reduce light, coat vegetation, alter food resources for filter feeding benthic-
mvertebrates, clog gills. In addition, sediment deposition may smother important spawning habitat
and adversely affect the abundance of food resources (benthic invertebrates). '
Nutrient Loading
Nitrogen and phosphorus, present in inorganic forms, provide a fundamental source of nutrients for "'
the growth of algae and Vascular macrophytes. Nitrogen contributions to the Mid-Snake River include
nitrates in spring flows, limited instances of nitrogen fixation by blue-green algae, ammonia and
nitrates in irrigation returns; animal wastes from feedlots and hatcheries; and municipal and industrial
point-source discharges. The phosphorus mines and generally phosphorus-rich rock formations in
southeastern Idaho are a source of phosphorus for the Snake River. Increased productivity in the
stream results in some decrease of oxygen concentrations in pools within the mainstem.
Analysis Plan
For this risk assessment, the focus will be on water quality/including temperature, dissolved oxygen
nutrients, coliform bacteria, and ammonia toxiehy. Idaho's water quality standards will be used as
measurement endpoints.
The ecological risk assessment methodology will be based on a mass balance water quality model
Elements of risk will be derived from uncertainty and variability in driving forces and from
uncertainty in the mass balance model. The water quality model developed by Yearsley (1991), uses
material and energy flows, and employs standard kinetics to simulate temperature, dissolved oxygen,
nitrogen, phosphorus, and primary productivity for time scales of hours to decades, vertical length
scales of 1 to 10 meters and horizontal length scales of hundreds of meters to hundreds of .kilometers.
The methodology will be used to develop measures of the risk of exceeding the state's water quality
standards before and after source control or mitigation. The probability densities are estimated by
Monte Carlo simulation, using variability and determined from available data. Model uncertainty will
be determined by comparing simulation results with measurements obtained in comprehensive field
studies.
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Middle Snake River Watershed Ecological Risk Assessment
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INTRODUCTION
The Snake River is the tenth longest river in the United States, extending 1,667 kilometers from its
origins in Western Wyoming to its union with the Columbia River at Pasco, Washington (Figure 1).
Along the way, it undergoes an elevation drop of about 2,895 meters. Its watershed encompasses an
area of.approximately 267,000 square kilometers (km2) in the States of Idaho, Oregon, Wyoming,
Nevada, Utah, and Washington. Before the 1960s, the Snake River was the most important drainage
in the Columbia River system for the production of anadromous fishes. .
The river reach of concern, hereafter referred to as the Mid-Snake River, spanning roughly 100 km,
lies in the west-central Snake River Plain of southern Idaho. This reach was selected by the local
counties and the state as the most severely degraded stretch of the Snake River in Idaho. The upper
end was defined by Milner Dam. Since, almost the entire flow of the Snake River is diverted at this
point it seemed like a reasonable point to characterize the river system. The downstream point is a
natural change in the river system, where flow direction changes from a northly direction to a westerly
direction. ' , , '
The contributing watershed includes 22,326 square km (Figure 2) of land below the Milner Dam and .
adjacent to the study reach. As a result of human activities spanning the past century, water quality
and biological resource problems have developed in the Mid-Shake River and its tributaries.
The demands on the water resources have transformed this once free-flowing river segment to one
with multiple impoundments, flow diversions, and increased chemical and microbiological pollutant
loadings; Physical changes include significant alterations to rapids and pool areas of the river.
Resulting biological changes include loss of native macroinvertebrate species, an invasion and
dominance of exotic species,.an expansion of pollution-tolerant organisms, and excessive growth of
macrpphytes and algae. '
The rapid rate of human population growth projected for the south Idaho region, as well as an
increasing demand for energy, irrigation resources, springs, and dairy feedlots, will place additional
burdens on an ecosystem that already has been substantially changed by human activity during this
century. ' ' /. .-•••:
This ecological risk assessment was undertaken to address such concerns by analyzing the Mid-Snake
River's stressors and resulting ecological effects and to stimulate broader public awareness and
participation in .decision-making for reducing ecological risks.
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WATER RESOURCE PROJECTS
: He»CT»«Mr«; S.OOq arrc it '
l"«»c»: l.OOO KW r«<«-.) .-jpariiy
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4. U>isl
20. Caieadt 35_
21. C. tan Kan «Q^
22. Ctana Cc««k 41*
23. Piddaek VtlUy 42.
24. «lll«« C«««k «3-.
25. i«llr C«a«k 44.
26. »t«»er Vall«r 45.
27. «ar« S«ci»(< 4i.
21. 0*yha« 47.
29. Slack Caayo* 46.
30. 0«a SO.
32. riaataat Vallay SI.
33. S«»« rails S2.
34. M.bbaea- S3.
35. Laka L«»afI * S4.
3e. Saekar C>aak 55.
37. »«t«l«a«
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little lead
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tmim Lakes
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Halad )
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56.
57.
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60.
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Figure 1. Water Quality Control and Management of the Snake River Basin: 1968 (reference -).
' Middle Snake River Watershed Ecological Risk Assessment
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V i }
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USGS Hydrologic Basins
Figure 2. Mid-Snake River Basin showing the outline of the U.S. Geological Survey Hydrologic Unit for
the Mid-Snake River Watershed.
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Middle Snake River Watershed Ecological Risk Assessment
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1.0 PLANNING
The ecological changes in this watershed have been observed by local, state, and federal agencies, by
academic researchers, by private organizations and businesses, recreational users, and by individuals
concerned about the loss of a species-rich lotic environment, an important cold water fishery, and
general water quality degradation in the Mid-Snake River. The perspective with which local! state,
and federal planning agencies, scientists, and the general public view this watershed is changing as'the
community becomes more aware of the impacts of the activities in the watershed on the ecology of the
rivpr ...._.
river.
A number of specific short term objectives and long term goals have been identified for the'purpose of
designing the watershed ecological risk assessment. The assessment was also designed to ensure that
assumptions, methodologies, and conclusions are scientifically valid, this section describes the risk
management team, regulatory, and non-regulatory activities mat are currently underway in this
watershed, as well as management goals and objectives. " .
1.1. Public Private And Governmental Groups Active in the Mid-snake River
Watershed
The development of a comprehensive watershed management plan involves close coordination of •'-'••
government, public, and private interests. Several working groups have been formed to address both
regulatory and nonregulatory issues. The agencies and organizations which have been identified as
active in decision making and management activities for the Mid-Snake River include federal state,
county, and private organizations, academic researchers, and interested citizens. The complete list of
active interests are given in Appendix A. •
1.2 Planning Process «
During preliminary development of the watershed ecological risk assessment for the Mid-Snake River,
a variety of programs were undertaken to identify those interested in the area and to help identify
pivotal considerations and ecological conditions needing protection in the watershed. A number of
planning efforts have been initiated by county officials (Mid-Snake River Planning Group)and state
agencies. Most of the planning efforts are directed toward restoration of the cold water biota! and a
reduction in aquatic plant biomass in the Mid-Snake River. Details of these activities are described.in
Appendix B.
Since 1969, several programs have been implemented to improve water quality in the Snake River
Basin. The activities have included the advancement of best available technology at the municipal
sewage treatment plant, regulation of waste handling at cattle feedlots and food processing industries,
and the initiation of best management practices on agricultural land through both state and federal
programs. Important federal, state and county regulations affecting the Mid-Snake River watershed
are discussed in Appendix B. ,
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1.3 Management Concerns And Goals For The Ecological Risk Assessment
s *
In addition, to advancing the science of risk analysis, this assessment is also undertaken to ensure that
the public aqd special interest users, government agencies, and scientists understand the problems and
that they develop a sense of partnership in reaching solutions for the recovery and protection of the
Mid-Snake River ecosystem. Too often, when such groups act in isolation, the problems remain
unresolved and each group becomes eptrenched in its own rhetoric and territoriality. Such a
consensus-building method of reaching shared solutions is inherently slow but fundamentally
democratic. Recognizing deadlines, limited resources, and the continued decjine of the habitat it is
important that progress be apparent. Therefore, the immediate plan calls for meeting the short term
goals, as well as holding periodic workshops to provide a forum for reaching some resolution of long
term goals.
The short-term goals for this watershed are associated with, and largely driven by, the specific
requirements of state and federal environmental legislation and the development of comprehensive
land-use plans at the county level. The reduction of aquatic macrophytes which interfere with
recreation (boating and fishing is the goal of the people in the watershed.
The short-term objectives for this watershed are: •
»• The establishment of total maximum daily loadings for water quality limited segments
of the river
* The review of permits for licensing existing and proposed hydroelectric projects
»• The evaluation of management plans for identification and control of nonpoint source
pollution .
»• Assisting in the writing of permits for National Pollution Discharge
The general management goals, for this watershed include several specific objectives: 1) attainment of
State Water Quality Standards (described in Appendix), 2) designation as a protected area, 3) sustained
economic activity in the region, 4) water for hydropower needs, 5) water for irrigation, 6)
conservation of wildlife and game species, 7) recovery of endangered species, and 8) recreation.
These managment goals and objectives are also determined by the state of our knowledge of the
ecosystem and our ability to develop simulation models for the flow of energy, materials, and
information between ecosystem compartments. At present we are able to apply the methodology to a
limited part of the ecosystem only. '
The long-term goals for the risk analysis are to 1) develop an ecosystem perspective for environmental
planning that can be used in other river basins throughout the region, 2)increase the knowledge of the
'structure and function of the Mid-Snake-River ecosystem, and 3)expand the scope of our simulation
methods to include more complex compartments in the ecosystem.
Middle Siiake River Watershed Ecological Risk Assessment
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1.4 Scope, Complexity, And Focus of The Ecological Risk Assessment
The approach.used to understand the interaction of sources, stressors, and resources on the Mid-Snake
River includes (1) field studies and experiments to increase our understanding of the Mid-Snake River
ecosystem, (2) characterization of ecological risk using mathematical modeling methods, and (3)
development of comprehensive management plans through the cooperative efforts of local, state, and
federal agencies, academic researchers, and an informed public. These measures alone cannot return
the Mid-Snake River to its original'state, but they can provide a better environment for the natural
• heritage resources which have survived. Furthermore, if this approach is successful, the Snake River
can provide an example for environmental stewardship in other river basins.
' ' ' ' ' - ' '"
Problem formulation for watershed-level risk assessments includes characterization of the watershed
and description of the stressors, ecological resources potentially at risk, and the array of ecological
effects. A critical component of the problem formulation is the identification of policy goals, societal
and natural resource values, assessment endpoints, and measures of exposure and effect. These are
linked in a manner that supports evaluation of the watershed's susceptibility to impacts, as well as the
development of a conceptual model of stressors and their effects with hypotheses that can be evaluated
and adjusted after the implementation of solution strategies. In the case of the Mid-Snake River, the
qualitative relationships between predominant stressors and their ecological effects were known before
initiation of this study and a variety of measures to counteract or alleviate their ecological effects were
in progress. Development of the problem formulation was substantially aided by consolidating and -
reordering existing data from a risk assessment perspective.
The focus of this ecological risk assessment is to define the interactions and interrelationships between
four principal stressors and their ecological effects. The stressors are:
•*••-'. Physical stressor - loss and alteration of the lotic habitat
»• Physical stressor - flow alteration (volume and rate)
*, ' ' Physical stressor,-sediment loading
r Chemical stressor - nutrient loading '.- .
The remainder of the problem formulation discusses linkages among these stressors, ecological effects
of these stressors, and the rationale for assessment and measures that will be analyzed to provide
direction for management activities in the watershed.
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Middle Snake River Watershed Ecological Risk Assessment
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2.0 ASSESSMENT OF AVAILABLE INFORMATION
This section describes the physical, chemical, and biological characteristics of the Mid-Snake River, :
including its hydrology and uses of the resources found within the watershed. A discussion of
ecological effects observed in the watershed and known or potential stressors that may be related to
those effects is also included in this section. .
Throughout 1992, 1993, and 1994, Idaho State University and the University of Idaho have been
conducting field Surveys and in-stream testing to describe the present physical, chemical, and
biological condition of the Mid-Snake River. These studies are targeting previously identified stressors
to quantify their impacts on the river. • • '•
•> ' , •
2.1 Characterization of Ecosystem at Risk
The Mid-Snake River as discussed in this study extends from Milner Dam (Rkm 1,028) to King Hill
(Rkm 877.6). Figure 3 shows a schematic diagram of the Mid-Snake River, including the locations of
all dams, tributaries, inflows, and water withdrawals.
2.1.1 Demographics •«•'•••
The geographic boundaries of the study area includes five Idaho counties (Twin Falls, Jerome, V
Gooding, Owyhee, and Elmore). This area is commonly referred to as the Magic Valley. About
136,831 people (85 percent of the population of the State of Idaho) live along the Snake River through
the southern portion of the state. The five largest municipalities in the Mid-Snake study area are Twin
Falls (27,951), Burley (8,984), Jerome (6,529), Rupert (5,455) and Hailey (3;687) (Figure 4). The '
remaining population (42.1 %) lives in unincorporated areas. "
2.1.2 Land Use
-, " . , '
Early settlers used water from the Snake River tributaries for irrigation. In the summer of 1903, the
Twin falls south side Land and Water Company tract was opened to farmers (IDEQ, NMP, 1994) for
irrigation of their crops. The Twin Falls North Side Land and Water Company was granted
permission to construct canal systems under the provisions of the Federal Carey Act in 1907.
Today, agriculture and grazing are the predominant land uses along the Mid-Snake River (Figure 5).
Irrigated crop production is made possible by the canal system originating at Milner Dam. Hay, grain,
potatoes, beans, and sugar beets are the principal crops produced on the irrigated croplands, while
wheat is the major dryland crop. Forest and urban land make up less than 7% of the total land use.
About 26 percent of the land is privately owned, 70 percent is federal land, and the remaining 4
percent is state land. - . ' .
"Idaho is one of the primary rainbow trout producers in the U.S. The trout farms along the Mid-Snake
River between the cities of Twin Falls and Hagerman produce 70-80 percent of the commercial trout
in the United States. Primary and secondary recreation in the area includes fishing, boating, and
swimming in some limited areas. ' -
DRAFT—June 17, 1996
-------
Blue Uk» Spnng
RM6O9.9
6<» Canyon Spnng RM 588.3
RadcCnMk,,RU£06.4
CwHrOtw RMS99.1
MudClMk RM591.7
OMpCiMk RM591J
RMS8&S
Figure 3. Schematic Diagram of the Middle Snake River.
10
Middle Snake River Watershed Ecological Risk Assessment
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MI d.d -1 e . S n a.k e River
S tudy Area
Figure 4. Map of Idaho showing the five counties surrounding the Middle Snake River study area
(highlighted).
DRAFT-Ju>ie'17, 1996
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2.1.3 Meteorology .
The climate of the region is semiarid, characterized by low annual rainfall, moderately hot summers
and cold winters. Mean air temperatures for the period 1951-73 at Twin Falls, Idaho (Rkm 982) were .
-1.4°C for January and 22.6°C for July, respectively. In the summer, air temperatures in the Snake
River canyon in the Mid-Snake segment are commonly in excess of 38°C. Annual precipitation
averages 26.67 cm ± 13.3 cm. Precipitation is fairly evenly distributed throughout the year, except
for July, August, and September when mean monthly rainfall is .635 cm, 1.067 cm, and 1.397 cm,
respectively. Since 1988, the area has experienced 6 years of low rainfall resulting in drought
conditions.
2..1.4 Geology .
The Snake River Plain comprises approximately 41,000 square kilometers of the Snake River Basin in
southern Idaho. The Snake River Plain (Kjelstrom, 1992) is subdivided into two geographic units, the
eastern plain and the western plain. The boundary between eastern and western plains is near King
Hill, Idaho (Snake Rkm 877.6). The Mid-Snake River segment (Rkm 1028 to Rkm-923) lies entirely
within the eastern unit of the Snake River Plain..
\ •' •
The Snake River Canyon was scoured by overflow from the Lake, Bonneville during the Pleistoene
approximately 15,000 years ago. The flood waters deposited sand bars"and gravel with boulders of
over 3 meters in diameter. Many rapids and waterfalls are formed by these boulders. Four major
waterfalls occur in the Mid-Snake reach over basalt ledges: 1) Shoshone Falls at 65 meters,
2) Twin Palls at 130 meters , 3) Star Falls at 36 meters and Auger Falls, a cascade which drops 55.
meters. The Snake River then enters a deep (20-90 m) canyon cut through lava and overlying
sedimentary deposits and continues for 151 km to King Hill. The geologic units include pleistocene
and older basaltic lava flows, pillow lavas (formed by lava flowing into water) alluvial deposits, and
lake deposits from ancient lakes.
Downstream of Twin Falls, Idaho, the Snake River canyon widens into small areas of bottom land and
terraces.. The largest of these areas is the Hagerman Valley, approximately 10 kilometers long and •
from 2 to 6 kilometers in width.
2.1.5 Hydrology
The Mid-Snake River is a managed system. The hydrology of this system is both the problem and
potential solution to biological changes which have evolved since it was a large lake. The hydrologic
units of the Mid-Snake River study area are shown in Figure 2. Water resources in the Mid-Snake
include precipitation, flow below Milner Dam, tributaries within the reach, ground water flow and
irrigation return flows. ; .
The upstream boundary of the Mid-Snake is at Milner Dam (Rkm 1,028) where until recently the
entire river was diverted for agricultural use during the irrigation season (April to October). In 1992,
an operating license issued by the Federal Energy Regulatory Commission (FERC) to Idaho Power
required that Milner Reservoir be kept full and a target flow of 6 cubic meters per second (cms) be
released, if available. Long term average annuarflows at Milner, just downstream from the diversion
and prior to the issuance of the FERC license, were 97 cubic meters second. The Snake River above
DRAFT-June 17, 1996 • 13
-------
IDAHO
Coarse Land Cover Groupings
(Idaho Dept of Water Resources)
Surface gravity irrigation
Sprinkler irrigation
Dryland agriculture
Rangeland
Forest
Riparian
Exposed rock
Urban
Water
Figure 5. Land Management on' the5nake River,. Idaho. '
-------
-------
Milner has an average annual flow of about 6xl09 mVyear. Below Milner diversions however the .
average flow is 3x10 m per year, ranging from several million to 0.6xl09 mVyear. In drought years-'
the flow at Milner is comprised almost entirely of withdrawal from American Falls Reservoir (about '
8.5 m /sec). With some gain from ground water and irrigation returns, the flows at Milner range
from 11.3m3/sec to 25.5m3/sec. When Lake Walcottand Milner'Reservoir are being filled or when
diversions begin, flows passing Milner are negligible (IDEQ NNM 1994). Flows at Milner are
regulated by climate (droughts) and irrigation withdrawals.
Downstream from Milner, flows increase substantially due to ground water discharge. The eastern
plain is underlain by a' thick sequence of volcanic rocks that store and yield large volumes of water,
comprising the largest and most productive aquifer in the Northwest. The Snake River incises the '
Snake River Plain Aquifer just upstream of Twin Falls, near Kimberly. Greater than 80 percent of the
aquifer emerges as spring water in the Thousand Springs area breaking through hundreds of seams or
cracks in the basalt layers of the canyon walls (Travis and Waite, 1964). Mundorff et al. (1964) found
that the total gain from the aquifer to the Snake River between Milner Dam' and King Hill about two
thirds of the discharge measured at the U.S. Geological Survey gage at King Hill. During the '
irrigation season when most of the river is diverted, the springs are the primary contribution to flow.
Water budget analysis for the entire Snake Plain has been described by Kjelstrom (1992). Kjelstrom
(1992) estimates that in water year 1980 ground water contributed 146 cubic meters second of flow to
the Mid-Snake River segment. This represents more than 50% of the-'av«rage annual flow at Lower
Salmon Falls. Kjelstrom (1992) reports, however, that ground water discharge to the Snake River has
varied as recharge conditions have changed. Frorri 1902 to the early 1950's, ground water discharge
to the Mid-Snake River segment increased due to recharge from flood irrigation on the north side of '
the Snake River. . .
In the 1950's the estimated average annual ground water flow to the Mid-Snake exceeded an estimated
190 cubic meters per second. Since that time flows have declined due to drought conditions in the
basin and increases in ground water piimpage from the Snake plain aquifer (Kjelstrom, 1992).
2.1.6 Fish
Prior to the development of hydropower on the Snake River, the Mid-Snake was host to a variety of
anadromous fish species extending up to Shoshone Falls. Shoshone Falls acted as a natural barrier for
Snake River fish and fauna. There were approximately: 24 native fishes below Shoshone Falls (Rkm
984) in the subbasin and 14 above the falls (Appendix C). Runs of fall and summer chinook salmon
(O. tschawytscha), steelhead trout (O. mykiss), and schools of pacific lamprey (Lampetra tridentatus)
migrated upriver as far as Shoshone, Falls each year. The anadromous salmonids were first severely
impacted by the construction of Swan Falls Dam (RKm 736.9. The final major hydroelectric events
resulting in the termination of migrating fishery stocks were the sequential closures of the Bliss Dam
(RKm 902,8; 1949), C. J. Strike Dam (Rkm 792.1; 1952), and ultimately the Hell's Canyon Projects.
The completion of these facilities terminated lamprey, salmon and steelhead migration into the'Mid-
Snake area. (Smith 1978, Bowler 1992). - The Snake River runs of fall chinook salmon and
spring/summer chinook salmon were listed as endangered USFWS, 1995. According to the US Fish
and Wildlife Service draft Recovery Plan (1994), it is hoped that remedial actions to protect fish and
wildlife endangered snails in the Mid-Snake may also benefit the recovery of these fish stocks in the
lower Columbia River.
14 .. • Middle Snake River Watershed Ecological Risk Assessment
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The large (> 68 kg) white sturgeon (Acipenser transmomanus) which is distinct from sea-run stock
found in the lower Columbia River also was extremely abundant prior to dam construction. The' race
of white sturgeon is now confined to tailwater reaches behind the many large hydroelectric dams. The
Shoshone sculpin (cottus greenei) and white sturgeon are federal candidate species for listing and Idaho
state species of special concern, respectively. .
The majority of the remaining fish in the Mid-Snake are impoundment or eutrophic tolerant species,
such as some catostomids (suckers), northern squawfish {Ptychocheilus oregonensis), the non-native
European carp, and various other cypririids (see Appendix C).
2.1.7 Invertebrates .
The historic diversity for native molluscs in the river was nigh at 42 species including 27 species of
snails in seven families and 15 species of clams in 3 families (USFS Draft Recovery Plan). Most cold
water natives only survive in limited spring-fed areas in the Mid-Snake River. The preferred "habitat
for cold water biota is temperatures less than 17" C with minimal sediment in free-flowing water.
Research by Frest & Johannes 19.. indicates that cold water invertebrates were most likely to be found
adjacent to rapids, near spring-influenced sites or near the mouth of major tributaries.
The following species are listed under the Endangered Species Preservation Act as threatened,
endangered, extinct or candidate: ' „ . ' ,
Threatened: . .
(1) the Bliss Rapids snail, Tayiorconcha serponticola (Hersnler, et al., 1994)
(2) the Utah valvata snail, Valvata utahensis (Call)
Endangered: . '
(3) the Snake River physid snail, Physa natricina
(4) Pyrgulopsis idahoensis
(5) the Banbury Springs limpet (undescribed Lanx sp.)
Candidate:
(6) the California Floater, Anodonta califomiensis .
(7) the Giant Columbia River Limpet, Flsherola nuttalli '.
(8) the Columbia River Spire Snail, Fluminicola columbiana
The Banbury Springs limpet, Snake River Physa, the Bliss Rapids snail, and the Idaho Spring snail are
found nowhere else outside of the Mid-Snake River. They are endemic to the ancient Lake Idaho,
which once covered most of the area during the Pliocene. The exotic hybrid Potamopyrgus
antipodarum is now the dominant mollusc as well as the dominant benthic organism in the.reach.
The benthic community (see Appendix C ) is dominated by a few taxa indicative of degraded
conditions (Dey and Minshall 1992). These taxa include Potamopyrgus, Chironomidae, Oligochaeta,
zndHyallela.
The large freshwater-clam, Margaritiferafalcata* once a food staple for Native Americans along the
River, is'now virtually eliminated from the Mid-Snake. This is a direct result of the extinction of
salmon runs in the area, as M. falcata larvae require salmon as a preferred host during their brief
• ' .!
DRAFT—June 17. 1996 15
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giochidial attachment stage. The decline in the .population in Mid-Snake may be due to sedimentation.
Vannote and Minshall 1982. Although M. falcata is common in the Bigfoot River and elsewhere in'the
Upper Snake, the species has been replaced by the smaller pelecypod, Gonidea angulata (Bowler and
Frest 1992) in the Mid-Snake.
2.1.8 Vascular Macrophytes and Algae
The vascular macrophytes cover up to 40% of the benthic habitat in some reaches. The dominant
species are Ceratophyllum demerswn and Potamogeton pectinatus. These species are generally
associated with well buffered, nutrient rich waters (Filbin and Barko, 1984; Best and Mantai 1978).
Blooms of planktonic (Microcystis, Cyclotella (the spring dominant), and Ceratium), periphytic, and
epiphytic algae Cladophora, and Hydrodyction, occur continuously during the spring and summer.
The total epiphytic algae and vascular macrophytes biomass may exceed 2;000 g/m2 dry weight with
the epiphytic alga (Cladophora) averaging 50% of the plant biomass in summer months (Falter, et al.
1995). ;
.••••. . -."«*'.
Massive growth of vascular macrophytes and epiphytic algae may be restricted by factors such as
flow, velocity, sediment composition, and nutrient availability. The changes if these parameters in the
Mid-Snake are believed to be the reseason for the uncontrolled growth olmacrophytes. Chapman
Consultants (1991) and Chambers et al (1991) observed that flows of greater than 1-2 meters per
second will limit vascular macrophyte growth. A reduction in sediment deposition (substrate),
increased light and associated nutrients would result in decreased plant growth, Ceratophyllum has
very limited below ground biomass and appears to absorb most of its nutrients through its leaves and
stems.- -.-.•. - • ' ' . •. ' ' (' - , ' ,
2.1.9 Wetland and Riparian Vegetation and Waterfowl
A brief description of the wetlands and riparian ecosystems is described. However.,, they were not
addressed in this phase of the risk assessment, The short term goals of the community are associated
with restoration of the open water system . Further iterations of the assessment will address the long
term goals. Most of the land adjacent to the Mid-Snake River has been used for agriculture, roads,
golf courses, small cattle operations, private homes, boat docking facilities, and fish hatcheries. The
remaining narrow band of riparian vegetation is dominated by two major plant communities (IDEQ,
Nutrient Management Plan, 1994). These are the sagebrush/grass cold-desert community and the
.scrub wetlands associated with free-flowing rivers and streams (B&C Energy 1984). There: are bands
of cottonwood groves, especially on the islands. A list ofplnat species identified in the watershed is
included in Appendix C. ,
The Mid-Snake River watershed is a waterfowl breeding and nesting habitat for white pelicans,
herons, cormorants, redtailed hawk, and kestrel. It is a major winter breeding area and migration
corridor for waterfowl using the Pacific fly way. The riparian area is a critical habitat for Waterfowl,
upland game birds and raptors because, of the lack of extensive forests.
The area provides wintering and nesting habitat for bald eagles (Haliaeetus leucocephalus) (Final
Environmental Impact Statement, Federal Energy Regulatory Commission, July 1990). According to
16 • Middle Snake River Watershed Ecological Risk Assessment
-------
the Bureau of Land Management the number of Bald Eagles in the Milner Dam to Bliss, Idaho area
ranged from 0 to 10 adults and juveniles.
2.2 Ecological Effects
A number of ecological effects resulting from the individual or synergistic influences of the principal
stressors (loss of habitat, flow,.and volume;;and increased sediment and nutrient loading) pose
significant secondary stress to the ecological integrity of the Mid-Snake River. These are:
»• Excessive algal and vascular macrophyte production
+ Exceedance of water quality standards for phosphates and temperature
> Decline in native aquatic species . ..
«• Growth of pollution tolerant and exotic aquatic species
The decrease in flow due to agricultural irrigation diversion and hydropower has resulted in both direct
habitat disturbance (e.g., loss of riffles, rapids, and pools that were important habitat to cold water
fauna) and secondary habitat disturbance (e.g., sedimentation in benthic habitats previously scoured).
This results in aquatic macrophyte invasion and dominance in waters that were previously too deep or
swift to support significant macrophyte growth).
Development of the watershed has also resulted in changes to the physical environment within the
stream as well. Impoundment with numerous dams has blocked the free run of the river to
anadrbmous salmonid species and has resulted in creation of landlocked populations of Pacific sturgeon
as well. Figure 6 shows a conceptual diagram of the river continuum of alternating lotic and lentic
habitats typically found in unimpounded streams of this region.
Several species offish and benthic invertebrate species are becoming increasingly rare or have
disappeared from pools-or rapids within the stream. Included among these are several indigenous cold
water species (see Appendix C). • • •
While a number of impoundments presently block the migration of ahadromous salmonids, a number
of resident coldwater species including trout and sturgeon have survived in the river and tributaries.
However their numbers are dwindling because of habitat losses. Critical habitat for spawning and the
forage base required for their survival are disappearing as a result of dewatering, sedimentation,
diminished flow, low dissolved oxygen, and elevated water and benthic temperatures.
Impoundments and flow modifications create additional water quality problems. The combination of
slower velocities and higher temperatures creates an optimal environment for the growth of plankton
and vascular macrophytes. •. .
DRAFT—June J7. 1996
17
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18
Middle Snake River Watershed Ecological Risk -Assessment
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Rapids
(lotic)
Pool
(lentic)
decrease
\
Pool
(lentic)
gravel
Figure 6. Illustrations of rapids and pools in a river system.
DRAFT-Jwie 17. 1996
19
-------
The vascular macrophytes provide substrate for the growth of-filamentous algal epiphytes, Cladophora
sp.- and Hydrodycton sp., which now form dense mats, and obstruct gas exchange with the atmosphere.
The dense growth of the vascular macrophytes, epiphytes, periphyton, and even phytoplankton are all
indicative of a system that has been overly enriched with nutrients,. Diminished water flow and
increased sediment deposition have resulted in shallower depths, lower turbidity and increased light
penetration. These are conditions which are highly conducive to vascular macrophyte growth.
Decreased flow velocities, loss of cobblestones and an increase in temperature have contributed to a
decrease in species diversity of benthic invertebrates. They are being lost as a result of alteration of
their habitat from dewatering, sedimentation, diminished flow, low dissolved "oxygen, elevated
temperatures, and pollution -all of which are incompatible with the survival of species acclimated to
cold water.
Eutrbphication is defined as the artificially enhanced or increased productivity of an aquatic system.
One of the main contributing factors of accelerated eutrophication is an overabundance of a limiting
nutrient such as phosphorus. . , .
Signs of eutrophication are particularly conspicuous during the summer when daylight is long in the
Twin Falls and Thousand Springs reaches of the Snake River, the area that is the focus of this report.
In this reach, water flows are so slow that the lotic environment is transformed into a lenthic or lake-
like condition. The much longer hydraulic residence times permit deVelbpriient of planktonic algae
and accumulation of soft bottom sediments, two conditions normally not associated with swift-flowing
streams. '-. . '.'•••
With .the increased degradation of the Mid-Snake River ecosystem there has been a concurrent rise in
the population of exotic species. The presence of these "biological interlopers" has severely impacted
the ecosystem. These include hatchery-raised rainbow trout (Oncorhyrichus mykiss), channel
catiish(Ictaluruspunctatus), carp (Cyprinus carpio), and Tilapia mozambiea, t. zillei, and T. nilotica
as well as non-native freshwater invertebrates (Potamopyrgus antipodarum and Corbicula).
2.3 Stressors
This section provides an overview of the primary and secondary stressors that are most likely
responsible for the degradation of the Mid-Snake River ecosystem! Of the three primary stressors \ ^'
identified, two of them are physical (flow alteration, sediment loading) and one is chemical (nutrient
loading). Although other physical, chemical, and biological stressors are mentioned in Table 1, it is
assumed that their importance will be minimized or eliminated if the key primary stressors are
removed. • '
2.3.1 Source of Stressors •
..Sources of stressors are directly and indirectly related to land use activities within the contributing
watershed and from hydrologic modifications to the river segment of concern. Table 1 summarizes
the primary sources of ecological stressors in the watershed. Table 2 characterizes the physical,
chemical and biological effects of these stressors.
2.3.2 Stressor Characteristics
20
Middle Snake River Watershed Ecological Risk Assessment
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There are four stressors (habitat alteration, sediment loading, nutrient loading, and flow alteration)
which cause primary or direct affects on the biota of the Mid-Snake River. .
Habitat Alteration. Almost any physical human activity can alter or destroy habitat with serious
consequences for the watershed. Physical habitat both in-stream and on adjacent lands is altered or
destroyed by activities associated with dam construction and operation. Riparian vegetation that
provides shading and overhanging habitat for invertebrate forage base is destroyed by urbanization,
clearing for agriculture and silviculture, livestock, and grazing. Riffles and rapids are usually altered
or destroyed by reduced flow levels due to operation and construction of dams and diversions. Roads
and their construction disturb both in-stream and watershed habitat. Sediment deposition and scouring
may alter habitat, obliterating or radically altering fish spawning habitats. Cattle grazing can destroy
both upland and in-stream habitat by the action of cattle trampling on destabilized land or in
streambeds. Dams fragment a river system, isolating resident fish in side channel (tailwater) reaches.
They may be stranded here and die or they are unable to reproduce because of inadequate habitats.
Table 1. Primary Anthropogenic Stressors Sources on the Snake River between Milner Dam and King
Hill, Idaho.
STRESSOR
Irrigated Agriculture
Fish Hatcheries
Hydroelectric Facilities
Point Sources
Confined Animal Feeding Operations
SOURCE
227,000 hectares irrigated with water withdrawn from the Snake
River
150,000 hectares irrigated with water withdrawn from the Snake .
River aquifer
Return flow from 13 streams and >50 surface drains
140 privately-owned •
4 state and federal . •
5 existing on mainstem
7 proposed on mainstem
Many on tributaries • • .
1 municipal sewage treatment plant
600 dairies and feedlots with waste equivalent to a population of
5,000,000 humans
Table 2. Stressor Sources and Characterization in the Mid-Snake River.
DRAFT—Juiti 17. 1996
21
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Table 2 (continued). Sources and Characterization in the Mid-Snake River.
SOURCE
TYPE
PHYSICAL
CHEMICAL
' Agricultural
Livestock Grazing .
Feed lots
Dry land , Fanning
!
Irrigated-
Agriculture
Habitat loss/alteration
Sedimentation '
Stream temperature Increase
Habitat loss/alteration
Sedimentation
Sedimentation
Sedimentation
•Flow alteration
Nutrient loading
BOD loading
Nutrient loading
BOD loading -
••«
Nutrient loading
Chemical
•contamination
Nutrient loading
BOD loading
Chemical
contamination
Habitat alteration
Urban
Land
Development
Road V
Construction
Combined Sewer
Overflow
, (CSO) and
Surface-Runoff
Sedimentation
Habitat loss/alteration
Stream temperature increase
Sedimentation
Habitat loss/alteration
Stream temperature increase
Sedimentation
Chemical
contamination
Chemical »
contamination
'Nutrient loading
BOD loading
BIOLOGICAL
*
Pathogens
Increased algal/macro-photic
production
Loss of riparian vegetation
Decreased macro invertebrate
richness and equitability
Pathogens
Increased algal/macro-photic
production
Loss of riparian vegetation
Decreased macro invertebrate
richness and equitabilitly ' . ' '•
Increased algal/macro-photic
production . • • •
Loss of riparian vegetation
Decreased macro invertebrate
richness and equitability
Increased algal/macro-photic' .
production
Loss of riparian .vegetation
Decreased macro invertebrate
richness and equitability
Exotic species
Loss of riparian vegetation
Decreased -macro invertebrate
richness and cquitabilily
Exotic species
Loss of riparian vegetation
Decreased macro •
invertebrate
richness and equitability
Exotic species
Increased algal/macro-photic
production
Loss of riparian vegetation
Decreased macro invertebrate
richness and equitability
22
Middle Snake River Watershed Ecological Risk Assessment
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TYPE .
SOURCE
PHYSICAL
CHEMICAL
Industrial/Point Source
Municipal
Wastcwater
Treatment
Aquaculturc
•• Hydroelectric
Power
Stream temperature alteration
Flow alteration
Stream temperature alteration
Row alteration
Sedimentation
Flow alteration
Stream temperature
alteration
Habitat loss/alteration
Nutrient loading
BOD loading
Chemical
contamination
Nutrient loading '
Industrial
BOD loading
Chemical
contamination
Nutrient loading
BOD loading
Chemical .
contamination
Loss of rcaeralion
capacity;
Nitrogen super
saturation;
Lowered. dissolved
oxygen :•
BIOLOGICAL
Loss of ecologically significant
species;
decreased algal/macro-phyte •
production
Loss of ecologically significant
species; •
Increased algal/macrophyte
production
Exotic species
Pathogens
Increased algal/macro-photic
production •
Loss of ecologically significant
' species
Loss of ecologically significant
species
Flow Alteration. Flow alteration results in both periodic increases and/or decreases in the usual
supply of fresh water to a river. Flow alterations include diversions, withdrawals, and impoundments.
The results of flow alterations, such as those on the Mid-Snake River, can be a variety of sources of
nonpoint pollution, including: ' ,
Changes in the timing and quantity of freshwater inputs downstream
»• Reduced downstream flushing
•• Sediment deposition-siltation of gravel bars and riffle complexes
» Erosion of the streambed and scouring in tailwater reaches
Increased deposition in areas of low water velocity resulting in formation of vascular
macrophyte beds and loss of fish spawning habitat
•• Increased downstream temperature ,
DRAFT-June 17, 1996
23
-------
»• Reduced downstream dissolved oxygen •
* , Velocity changes
Since there is considerable competition among the various users for water withdrawal rights, the
ecological integrity of the Mid-Snake River ecosystem is severely stressed by reductions in flow. This
is a particularly acute problem in the spring and summer months -because of irrigation diversions.
During the irrigation season (April through September) water above Milner Dam is diverted, resulting
in a minimum discharge of approximately 200 - 300 cfs from Milner. Some flow is returned from
irrigation during years of average rainfall; during low rainfall years, however, .this return flow may
stop altogether. Other sources of flow downstream from Milner Dam include springs .in the river bed
and several tributaries. .
Impoundments which store and divert water for hydropower and irrigation-result in flow
modifications in the mainstem and tributaries, there are five existing impoundments on the Mid-
Snake River: Milner, Shoshone Falls, upper Salmon Falls, Lower Salmon Falls, and Bliss Dam
(Figure I). Additionally, new impoundments, weirs, and diversions are proposed at Star Falls,
Kanaka Rapids, and Auger Falls (Figure 3). Falls or rapids in these areas are drowned by the elevated
water surface upstream of die dam, and aeration capacity of the-falls is lost. The backwater upstream
of these dams is slowed and may become stratified under relatively stagnant flow conditions.
Flow alterations in the Mid-Snake River result from multiple impoundments and flow modifications in
the mainstem, tributaries, and ground-water outfalls. In the Mid-Snake River, the river drops 488
meters over the 30Km distance of the river segment. Consequently numerous hydroelectric facilities
are located in this area. There are five existing impoundments on the Mid-Snake River: Milner,
Shoshone Falls, Upper Salmon Falls, Lower Salmon Falls, and Bliss Dam. Additionally, new
impoundments, weirs, and diversions are proposed at Star Falls, Kanaka Rapids, and Auger Falls.
These impoundments store and divert water for agricultural irrigation and hydropower generation.
Diversion dams and their associated impoundments for electric power production are installed at many
falls or rapids sites to increase the hydraulic head to power hydroelectric turbines. The backwater
upstream of these dams is slowed and often becomes stratified under relatively stagnant flow
conditions. Falls or rapids in these areas are drowned by. the elevated water surface upstream of the
dam, and aeration capacity of the falls is lost. : •.
The dynamics of flow influences the process of sediment suspension and deposition. Altered flows
change the pattern of sediment scouring and deposition by reducing downstream flushing and increase
the siltation of gravel bars and riffle complexes. Clear water released from dams results in increased
erosion of the riverbed and bank scouring occurs below dams, particularly in the littoral shoreline >
areas. These habitats are most often altered in ways that are not compatible with the survival of
benthic communities. - .
Sediment Loading. Sediment deposition has direct ecological effects on macro invertebrates by
blanketing important habitat with sediments and smothering species that depend upon aerobic
sediments. Finer sediments may clog the gills or feeding apparatus of species adapted for living in
coarser sediments. Sediment deposition may promote vascular macrophyte growth, alter the
, underlying sediments, and make them unsuitable for indigenous macro invertebrates. Fine sediment is
not functional as a spawning substrate for most species.
24 • Middle Snake River Watershed Ecological Risk Assessment
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Sediment in suspension may reduce light, coat vegetation, alter food resources for filter feeding '.
benthic invertebrates, clog gills. Sediment deposition may smother important spawning habitat-, and,
adversely affect the abundance of food resources (benthic invertebrates).
Sediment transport capacities are lower upstream .of impoundments since the velocity and turbulence of
river" currents is dissipated in the slowly moving backwaters of impoundments. Downstream of the
dams, the higher-velocity discharges erode banks and the river bottom and carry suspended sediment
to the backwaters of the next impoundment. The net result is deposition of suspended material
upstream of a dam and scouring of the river bottom arid shallow shoreline areas downstream of the
dam. . .
Poor agricultural practices from crop production and cattle feedlots can result in increased sediment
loading. The Soil Conservation Service's River Basin Reports of 1976, 1979, and 1981 identified ,
substantial areas of serious erosion on surface-irrigated lands in the Upper Snake River basin.
Gooding and Jerome Counties each had more than 20,000 hectares with erosion rates exceeding 1.8
metric tons/year, while Twin Falls County had between 2,000 and 20,000 hectares exceeding 1.8
metric tons/year. •
Sediment loads have been shown to increase dramatically as runoff flow rates from .cropland increase
(Carter, 1976). Greater rates of flow off the land into irrigation returns increase the amount of the
sediment inputs into the streams and river. Therefore, over-irrigation tends to exacerbate "soil erosion-
losses from tilled land. Irrigation return flows may carry pesticides, nutrient-rich fertilizers, and
sediment loads to the river. Runoff from individual fields, especially those irrigated by furrow
irrigation, carries sediment into drainage, canals, which eventually drain into the river. Different crops
yield different levels of sediment, e.g. sediment loss from alfalfa fields is fairly low while that from
dry-bean production is fairly high.
Most of the smaller canals that flow over the precipitous canyon wall percolate through talus debris
piles formed from rock falling off the canyon wall. As the water percolates through these debris piles
it drops much of its sediment load. Accumulated sediment and rock debris tend to remove many of the
other pollutants associated with irrigation wastewaters in a fashion similar to wastewatef treatment by
land treatment systems. During heavy rains or after snow melt, the overflow into the river occurs
with little or no percolation through debris piles. Most larger irrigation return flows are much more
damaging to the river. For example, irrigation return flows at the Perrine Coulee hydroelectric
facility at the canyon wall are conveyed through a penstock to a hydroelectric turbine. Thus, the water
bypasses the talus slope and is discharged directly to the river, creating a sediment-laden pollutant
plume in the river.
The most recent estimates of irrigation erosion are from the Soil Conservation Service (SCS) River
Basin Reports from 1976, 1979, and 1981. The reports identified substantial areas of serious erosion
on surface-irrigated lands in the Upper Snake River Basin. Gooding and Jerome Counties each had
more than 20,000 hectares with erosion rates exceeding 1.8 metric tons/ year, while Twin Falls
County had between 2,000 and 20,000 hectares exceeding 1.8 metric tons/ year.
Though some farmers have incorporated low till and other best management practices as part of their
cultural practices, implementation of best management practices is not widespread in the region.
Farmers'who incorporate low tillage practices may compensate for their assumed loss of high quality
growing conditions by heavy use of pesticides and fertilizers. Soil losses by irrigation runoff often
DRAFT—Jwi£ 17, 1996 . ' 25
-------
result in severe soil losses from poorly, managed lands and accumulations of soil on properly managed-
lands (Carter, 1976). Other sources of sediments in the Mid-Snake River include urban nonpoint -.
sources and stormwater runoff, cattle feedlots, housing and commercial development, road
construction* and sand and gravel operations. Chemical Stressors
Nutrient Loadings. Nitrogen and phosphorus, present in inorganic forms, provide a fundamental
source of nutrients for the growth of algae and vascular macrophytes. Phosphorus is generally the
.limiting nutrient in freshwater systems. Phosphorus must be available as soluble inorganic
orthophosphate. Nitrogen may be present as nitrate (NO-,.), nitrite (NO2_), ammonia (NH3),
ammonium ion (NH4+)« or gaseous nitrogen (N^. Though some organisms have' developed
extracellular enzymes or other means of liberating orthophosphate from organic matter, most vascular
macrophytes and algae must rely on the availability of inorganic orthophosphate in their environment.
In a river environment, available orthophosphate is quickly assimilated by plant life and converted to
tissue of is adsorbed onto soil particles, forming relatively insoluble complexes. Death of an organism
eventually results in its deposition on the bottom of a quiescent portion of the river along with other
phosphorus bound to soil particles. The phosphorus remains bound to soil particles until it is
chemically or biologically liberated under anaerobic conditions.
Nitrogen contributions to the Mid-Snake River include nitrates in spring flows, limited instances of
nitrogen fixation by blue-green algae, ammonia and nitrates in irrigation returns; animal wastes from
feedlots and hatcheries; and municipal and industrial point-source discharges.
The phosphorus mines and generally phosphorusrrich rock formations in southeastern Idaho are a
source of phosphorus for the Snake River.
Increased productivity in the stream, results in some decrease of oxygen concentrations in pools
within the mainstem.
Toxics. Chemical pesticides from agricultural operations (although not examined closely in this
assessment) may be potential stressors of aquatic and terrestrial organisms in the watershed'as well.
Pesticides are widely used on tillage crops in the watershed. ,
Antibiotics (e.g., sulfa drugs) are routinely added to feed and raceway waters as part of standard
management practice in fish farming. These antibiotics are used to protect the fish from routine.
infections, which may stunt growth, increase mortality, or affect the marketability of the fish. Little
information has been collected on their adverse ecological effects on natural biota in the Mid-Snake
River although published information suggests a detrimental effect on natural .bacteria and fungi
occurring in sediments and the water cojumn.
2.3.3 Secondary Stressors ,
Secondary stressors are an indirect effect.of the primary stressor. Increases in temperature, oxygen
decreases, increases of macrophyte and algal biomass are the result of the interaction of the primary
stressors. .
The three principal stressors are substantially linked in the way they work together to change the
ecosystem in the Snake River. Because sediment loading and transport are ultimately linked to
26 • . Middle Snake River Watershed Ecological Risk Assessment
-------
overland flow and stream velocity; the rate of flow is critical in influencing sediment affects and . '
ecological models should reflect these inter-relationships.
Attempts to control or mitigate any one of these stressors to sustain the ecological endpoints must
involve management of the other two. Similarly, management of the secondary stressors, such as
habitat impairment will require careful management of all three of the principal stressors.
Each of the three principal stressors (flow, sediment deposition and nutrient loading) contributes to the
development of one or more secondary stressors. For instance, all three pf the primary stressors can
have a direct ecological effect on the ecological assessment endpoint but the stressors also may create
yet another tier of stressor-effect (e.g..vascular macrophyte growth, sedimentation, and decreased
flow alter habitat for both cold water fish and benthic macro invertebrates). Table 2 summarizes the
.stressor sources and categorizes resulting stressors for,both primary and secondary sources by
type—physical, chemical, or biological.
Increased Stream Temperatures. Water temperatures tend to fluctuate over a greater annual range
because of the presence of numerous impoundments on the Snake River. .The increase in surface area
exposes more water to solar radiation which tends to raise summer surface water temperatures.
Maximum water temperatures have been established for impoundments along the river by state and
federal regulatory agencies to protect fish populations which have a low tolerance for warm water
temperatures. Temperature ecological effects are often cumulative atong the river. Heat absorbed at -
one site may not cause temperatures to exceed the allowable temperature at that site, .but the
cumulative effect of heat gained at successive reservoirs could raise temperatures beyond maximum
tolerable levels in the river. A secondary effect of warmer water is lowered dissolved oxygen
carrying 'capacity relative to cold water. Destruction of riparian vegetation and the shading it provides
can cause an increase in stream temperatures.
Biological Stressors. Over the last 30 years river flow and water quality have changed sufficiently so
that there are now frequent stands of vascular macrophytes and attached algae throughout the Mid-
Snake, including epiphytic and epipelic varieties. Rampant growth of vascular macrophytes which
peak during May to July has occurred as a result of nutrient loading and other agricultural nonpoint
source pollution. At least three species of vascular macrophytes, Ceratophyllum demersum, Elodea
canadensis, and Potaniogeton pectinatus, 'now grow in dense and obstructive stands in quiet pools
within the segment of interest. These species are associated with eutrophic waters even in the lotic
environment. . .
A number of biological changes in the stream and watershed have resulted from the physical and
chemical perturbations of human use. These biological changes may, in turn, function as stressors to
the remaining biological community. There has been a loss of endemic species of both fish and macro
invertebrates, as well as a concomitant appearance of exotic macro invertebrate and invertebrate
fauna, especially Potamopyrgus. The loss of riparian vegetation, which historically provided shade
and habitat along the water's edge has a detrimental affect on the Mid-Snake River ecosystem. There
has been a profound increase in phytoplankton and vascular macrophytes as well, altering patterns of
flow, characteristics of habitat, and availability of forage base by competitive exclusion of high quality
food preferred forage species. Inflow of man-made antibiotics from fish farm effluents may be a
source of stress on the endemic microbiota within the stream and natural sediments.
DRAFT—Jun* 17, 1996 • 27
-------
28 • Middle Snake River Watershed Ecological Risk Assessment
-------
3.0 ASSESSMENT ENDPOINTS
Assessment endpoints are explicit expressions of the actual ecological value that is to be protected
(USEPA, 1992) and thus form a basis for linkage to management concerns, measures of exposure and
effect, and risk management activities in the watershed. Assessment endpoints must reflect ecological
relevance. That is, an assessment endpoint should focus on an ecological component that is important
to the structure and function of the watershed ecosystem. ,
Endpoint selection is critical to the ecological risk assessment process because endpoints.must complete
a sequence linking environmental values, which are often abstract, to specific management actions that
will reduce risks to these values. The starting point of this logical sequence is the recognition of values
that need protection, expressed as management concerns.
Three assessment endpoints for the Mid-Snake River risk analysis are:
" The reproduction and survival of coldwater fisheries - particularly the trout and
sturgeon
*• •. The reproduction, survival,'and diversity of natiye benthic fauna
• > ' *
»• The growth of vascular macrophytes and green and bluegreen algae
Attainment of these ecological endpoints will protect much of the ecological system. Restoration of a
migratory salmonid fishery is not considered feasible because of the number of downstream
impoundments that block migration (Figure 1). •
Coldwater biota life support is selected as an assessment endpoint, for several reasons. The ecological
significance of this endpoint includes the fact that endangered species in the Mid- Snake River are
coldwater invertebrates and fish. The invertebrates and fish exhibit marked sensitivity to the stressors '
affecting the Mid- Snake River, and a coldwater biota endpoint can be linked quantitatively to several
environmental parameters (e.g., numeric criteria) to document stressor/ecological response
relationships.
In addition to the restoration' of invertebrate and fish species, the reduction in vascular macrophyte
biomass is essential to assure the restoration of cold water biota. The nuisance growths are
ecologically significant in displacing and/or stressing desired coldwater periphyton, phytoplankton,
fish, and macro invertebrates..
DRAFT—June 17. 1996
29"
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30 Middle Snake River Watershed Ecological Risk Assessment
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4.0 ANALYSIS PLAN
To achieve this assessment's objectives within the framework of the ecological risk assessment, we are
using a strategy that could be characterized as source-based control. While this strategy has elements
of the traditional approach to the allocation of waste loadings, it will contain elements of risk analysis.
The focus will be on water quality, including temperature, dissolved oxygen, nutrients, coliform
bacteria, and ammonia toxicity. The State of Idaho's water quality standards will be used as measures
of effect. The analysis plan for the ecological risk assessment of the Mid-Snake Watershed relies on
probalistic models. •
4.1 Assumptions
The modeling and analysis of ecological risks in the Snake River are based on a number of key
assumptions. These include the following: . .
•• Major features of the Snake River ecosystem can be described in terms of
• compartments between which there can be flows of energy, material, and information.
»• The flows of energy, material, and information tjetween ecosystem compartments can
be described mathematically within given bounds of'uncertainty.
> There is sufficient information to characterize the variability of environmental forcing
functions such as meteorology, hydrology, and water chemistry.
»• There is sufficient information to characterize the variability of forcing functions
associated with important types of human development on the Snake River,
> * Assessment endpoints for biological systems included in the risk analysis are known
within given bounds of uncertainty. Where endpoints are not known, surrogates, such
as water quality standards, can be applied. .
* The principal components of risk arise.from uncertainty or variability in driving
forces and from uncertainty in the models used to describe the state of the ecosystem.
4.2 Conceptual Model
The conceptual model of the river and associated areas will characterize the biological communities
and their relation to the specific water quality parameters to be examined in the ecological risk
assessment. This conceptual model would ideally include all levels of biological organization
(organism, population, community, and ecosystem), as well as physical and chemical descriptions of
the habitats.
The conceptual model for'this ecological risk assessment of the Mid-Snake River watershed
incorporates the descriptions of the ecological components, stressors, ecological effects, and exposure
DRAFT—June 17. 1996 • 31
-------
scenarios to assist in developing hypotheses regarding how each stressor may affect the watershed
Several submodels of water quality, river flow, and the aquatic communities were generated. ' -
i ' - " .
Figure 7 illustrates some of the critical interactions and the likely ecological effects on ecosystem
function. In this model flow controls the loading of both sediments and nutrients which in turn
influence macrophytic and algal productivity, detrital sedimentation, and habitat alteration for both
fishery and benthic fauna. Increased flow often increases sediment and nutrient loading but it also may
resuspend sediment deposits, and scour the streambed, and reduce the residence time of dissolved
nutrients. Decreased flow, while reducing the loading of sediments and nutrients, often results in new
net sediment deposition and greater nutrient retention times in the system, resulting in higher rates of
vascular macrophyte and algal productivity. Substantial deposits of sediments or large, dense vascular
macrophyte beds can slow downstream rates of water flow. '
Figure 8 illustrates the collective action of several stressors on the cold water fishery. In this
illustration, flow modification arising from a variety of diversions for anthropogenic use results hr
habitat alteration, chemical stress, and thermal stress on sensitive life stages of sensitive species.
Figures 9 and 9b describe in detail the ecological effects of sediment and nutrient loading on the
benthic invertebrate .fauna. ' .
Figure 10 illustrates the conceptual model of macrophyte growth in the Snake River. The model
describes the role of sediments on algal and vascular macrophyte growth, through increased surface
area for colonization, and increased fertility of the vascular macrophyte beds resulting in nuisance
growth of vascular macrophytes, periphyton, and epiphytes.
4.3 Measures of Exposure and Effect . .
Measures of exposure and effect are those characteristics or parameters of an ecological system that
may be measured to determine the status of an assessment endpoint or to provide information to
predict ecological effects on an assessment endpoint, when the assessment endpoint itself is not .
amenable to direct measurement (USEPA, 1992). Measures of exposure and effect endpoints are
chosen to quantify the Mid-Snake's stressor-ecological effects relationships, to determine loadings and
the magnitude of loading reductions needed to reduce risk; to develop defensible total maximum daily
loads, and to attain water quality standards. - . ..
The measures of exposure and effect listed below will be assessed relative to the two assessment
endpoints. Many of the measures of exposure and effect apply to both assessment endpoints.
Measures of exposure and effect related to survival and reproduction of coldwater biota (sturgeon,
trout, benthic macroinvertebrataes are: . . •'.'.''
»• Numeric water quality criteria for
—dissolved oxygen, temperature; ammonia, phosphorus, nitrogen, suspended
' sediments .
,• > • Physical measures of habitat structure and suitability
32 • . ''Middle Snake River Watershed Ecological Risk Assessment
-------
—channel morphology
»• Flow (volume, seasonal timing, and duration)
>• Presence, absence and abundance of cold water fish species
*• Benthic community diversity metrics
—macroinvertebrate populations, periphyton populations
Measures of exposure and effect related to growth of aquatic macrophytes and algae are:
•• Numeric water quality criteria for
—dissolved oxygen, temperature, ammonia, phosphorus, nitrogen, suspended
sediments ,
»• Metrics of vascular macrophyte community '.'.." •
—vascular macrophyte populations, abundance, biomass, composition, epiphytic
communities-biomass and composition
•• Metrics of plankton and periphyton communities
—phytoplankton abundance, composition, periphyton abundance, composition,
zooplankton abundance
»• Physical measures of habitat structure and suitability
—channel morphology, sediment volume, flow (volume, seasonal timing, and
duration), substratum characteristics
4.4 Simulation Modeling
The ecological risk assessment methodology will be based on a mass balance water quality model.
Elements of risk will be derived from uncertainty and variability in driving forces and from
uncertainty in the mass balance model. The water quality model developed by Yearsley (1991), uses
material and energy flows as shown in Figure 10. This model uses standard kinetics to simulate
temperature, dissolved oxygen, nitrogen, phosphorus, and primary productivity for time scales of
hours to decades, vertical length scales of 1 to 10 meters and horizontal length scales of hundreds of
meters to hundreds of kilometers.
This methodology will be used to develop measures of the risk of exceeding the state's water quality
standards before and after source control or mitigation. The concept is illustrated in Figure 11 where
the" probability density of total phosphorus is shown schematically before and after total maximum
daily loadings have been developed for nutrient sources. The probability densities are estimated
empirically by Monte Carlo simulation, using variability and uncertainty in driving forces as
determined from available data. Model uncertainty will be determined by comparing simulation
results with measurements obtained in comprehensive field studies such as those reported by Brockway
and-Robison( 1992).
DRAFT-June 17, 1996 33
-------
The ecological risk analysis for the middle Snake River is developed from the stressor characteristics'
and ecological effects identified in the formulation of the problem. Stressor characsteristics are
defined in terms of probability models for point source loadings, nonpoint source loadings, 'and
meteorologic and hydrologic conditions. These -characteristics are used as forcing functions for a.
mathematical model of the river ecosystem to develop cumulative distribution functions for
environmental factors such as dissolved oxygen, temperature and macronutrients. The cumulative
distribution functions will.be used to determine the risk associated with ecological effects to coldwater
species of fishes and benthic invertebrates. This will be done by overlaying the cumulative
distributions functions for environmental factors on the environmental requirements of important
coldwater species. . , '
34 ' Middle Snake River Watershed. Ecological Risk Assessment
-------
Figure' 7. A Conceptual Water Qualify Model of the Middle Snake River.
DRAFT-June 17, 1996
35
-------
Figure & Conceptual Model Describing Interactions of Stressors and the Effects on Cold Water Fishery in
the Middle Snake River.
36
Middle Snake River Watershed Ecological Risk Assessment
-------
Source
Agent
.(^tressor)
Exposures
Responses
. . -"point-sourca"
upstream
resuspenston/redistribution
irrigafion returns
runoffs
co-slressors
dissolved
>^*"^ jdcposmonT}
d substrate
•' Jla'itikxobial growth fbrxnicrobxal
IP AriamllniH ' lUMVill in W«
in W«UCT
sg_
A - .1
XMC PttPt ^POw
>|M -1 ?r-A*i^i ^iraf^^r u
cofanxmBOD • M cednnentBOp
Effects
.Stressors"
Exposures
« *
Responses
Effects
loss of sensitive loss of sensitive.''
species species
^placement/
altered species
distribution/
exotic species
altered new-water
thcnnal stress
onbcnihcs
Figure 9a. Protection of Endangered and Other Ecologically Important Benthic Invertebrate Species
(sediments).
DRAFT—Juiie 77. 1996
37
-------
CO
CD
2
I
CO
o
21 CO
'TT' 3 • C
*_ o to o
c So ex
Q> O O. CO
CD
CC
(O
ts
£.
UJ
o
CO
co
2
co
CO
I
CO
o
a.
en
0
.co
o
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CO
0>
DC
CO
4-*
u
G>
s
Figure 9b. Protection of Endangered and Other Ecologically Important Benthic Invertebrate Species
(nutrients). , . ,
38'
Middle Snake River Watershed Ecological Risk Assessment
-------
Figure 10. Conceptual Model for Macrophyte Growth in RBM10 as Applied to the Snake River.
DRAFT—June 17, 1996
39"
-------
&
Q
O
O
tf
e
d
ffl
O
02
ft-
BEFORE TMTIT
TOTAt PHOSPHORUS
AFTER
TOTAL PHOSPHORUS
Figure 11. A Conceptualization of Risk Outcome as Applied to the Development of a TMDL for Total
Phosphorus. •
40
Middle Snake River Watershed Ecological Risk Assessment
-------
5.0 REFERENCES
B & C Energy, Inc. 1984. Star Falls Hydroelectric Project, FERC No. 5797, Vol. 2, Exhibit E.
Environmental Report. Application for License for Major Unconstructed Project.
Best, M.D. and K.E. Mantai. 1978. Growth of Myriophyllum: Sediment or lake watars as the source
of nitrogen and phosphorus. Ecology 59: 1075-1080. .
Bowler, P. A., 1990. Rapid spread of the freshwater hydrobiid snail Pntamnpyrgiis ann'pndamm
(Gray) in the Middle Snake River, Southern Idaho. Prnnpifttlings nf thft Desert Fishes Council 21: 173-
182. Desert Fishes Council, P. O. Box 337, Bishop, CA 93514.
• ' *
Bowler, P. A., 19'92. Measuring river health through aquatic diversity: Theories, techniques and
case studies. In Ereparation: Dept. of Ecology and Evolutionary Biology, University of California
at Irvine, Irvine, California 92717.
Bowler, A. and P. Bowler, 1987. The history and heritage of the Hagerman Reach of the Snake
River.
Bowler, P. A., and T. J. Frest, 1992. The non-native snail fauna of the Middle Snake River,
Southern Idaho. (IN PRESS: Pmr nf th* rterert Fishcis rnnnril ?.?.-. P. O. Box 337, Bishop, CA
93514. ' ':'....
Brockway, C. E., and C. W. Robison. 1992. Middle Snake River water quality study" Phase 1.
University of Idaho, Idaho Water Resources Research Institute, Kimberly, Idaho. 70 pp.
Carter, D.L. 1976. Guidelines for Sediment Control in Irrigation Return Flow. April 1. USDA and
U of I Ag Res Station Environmental Quality Vol 5 #2. •
Chambers,?. A., E.E. Prepas, M.L. Bothwell and H.R.Hamilton. 1991. Roots versus shoots in
nutrient uptake by aquatic macrophytes in flowing waters. Can. J. Fish. Aquatic Sci. 46:435-439.
Chambers, P.A., E.E. Prepas, H.R, Hamilton and M.L. Bothwell. 1991. Current velocity and its
effect on aquatic macrophytes in flowing waters. Ecological Applications 1:249-257.
Chapman Consultants, Inc. 1992. Ecology of the middle Snake River and cumulative assessment of
three proposed hydroelectric projects. Appendix in: Application for license for Kanaka Rapids
hydroelectric project, Empire Rapids hydroelectric project Boulder Rapids hydroelectric project.
Dey, P.D. and G. W.Minshall. 1992. Middle Snake River Biotic Resources: A Summary of
Literature in the Snake River Water Quality Assessment Bibliographic Database. Vol.1. Final
Report to U.S. Environmental Protection Agency, Region 10.
DRAFT—June 17. 1996 ' .41
-------
Falter, C.M., C. Burris, J.W.Carlsqri, -and R. Freitag. 1993. Middle Snake River Productivity and-
Nutrient Assessment, Prepared for Division of Environmental Quality, Idaho Department of Health .
and Welfare. Idaho Water Resources Research Institute, University of .Idaho.
Federal Energy Regulatory Commission. July 1990> Final Environmental Impact Statement for
Milner, Twin Falls, Auger Falls, and Star Falls Hydroelectric Projects, Idaho. FERC/EIS-OQ48F.'
Federal Water Pollution Co'ntrol 'Administration: Northwest Region, 1968. Water Quality Control
and Management: Snake River Basin. Portland, OR. 72 pp.
Filbin and Barko 1984 . .
Frest, T. J., and E. Johannes, 1991. Mollusk fauna in the vicinity of three proposed hydroelectric
projects on the middle Snake River, Central Idaho. Final Report, Prepared for Don Chapman
Associates, Inc., Boise, Idaho. Deixis Consultants, 6842 24th Ave N.E., Seattle, WA 98115.
Frest, T. J, and P. A. Bowler, 1992. The ecology, distribution and status of relict Lake Idaho
mollusks and other endemics in the Middle Snake River. Tn Press ' r .'
Haynes, A,, B. J. R. Taylor, and M. E. Varley, 1985. The influence of fire mobility of Pjatamopyrgus
jftnkinsi (Smith, E. E.)(Prosobranchia: Hydrobiidae) on its spread. Arch Hydrnhlnl _lfB:(4), 497-
508. Stuttgart.
Hershler, R., T.J. Frest, E.J. Johannes, P.A. Bowler, and F.G. Thompson.; 1994. Two new genera
of ydrobiid snalis (Prosobranchia: Rissooidea) from the Northwestern United States. The Veliger
37(3): 221-234. • . . ! •
Idaho Fish and Game Department, 1953. The size and timing of runs of anadromous species of fish in
the Idaho tributaries of the Columbia River. Prepared for the U.S. Army Corps of Engineers, April.
Idaho Department of Health and Welfare, Division of Environmental Qua'lity. 1995. Draft Nutrient
Management Plan '
Jerome County Planning Department. 1984. Jerome County Zoning Ordinance. Jerome, Idaho.
Kjelstrom, L.C. 1992. Assessment of Spring Discharge to the Snake River, Milner Dam to King Hill,
Idaho. U.S. Geological Survey Water Fact Sheet Open-File Report 92-147.
Kjelstron 1986. Flow and characterization of the Snake River and water budget for the Snake River
Plain, Idao and eastern Oregon. USGS Open File Report
Minshall, G.W., C.f. Robinson, and T.V. Royer. 1993. Monitoring of the Middle Reach of the
Snake River: Nonpoint Assessment. Final Report. Submitted to the Idaho Divison of Enviromental
Quality, Twin Falls, Idaho. 76 pp.
42 ; ' Middle Snake River Watershed Ecological Risk Assessment
-------
Mundorff, J.J., E.G. Crosthwaite,' and C. Kilburn. 1964. Groundwater for irrigation in the Snake
River basin in Idaho. Water Supply Paper 1654. U.S. Geological Survey, Department of Interior.
224pp.
Ponder, W. F., 1988. Potamopyrgus antipodarum- a molluscan colonizer of Europe and Australia.
J. Moll. Stud. 54: 221-285.
Proc National Academy, Aci 79;4103-4107.- .
* ' •• i * '
/
Smith, G. R. 1978 . Biogeography of intermountain fishes. In: Great Basin Naturalist Memoirs.
Intermountain Biogeography: A Symposium. No. 2., pp 17-42. • '•
Stanford, 1942
Thomas, C.A. 1969. Inflow to the Snake River Between Milner and King Hill, Idaho. April I.
Travis, W.I. and H.A. Waite. 1964. Water resources in mineral and watr resources in Idaho.
Special Report No: 1 Idaho Bureau of Mines and Geology. . .
Twin Falls County Planning Department. 1987. Ordinance No. 21:'Comprehensive zoning plan and ;
regulations. Twin Falls, Idaho.
U.S. Environmental Protection Agency. 1976. The influence of land use on stream nutrient levels.
EPA Publ. #600/3-76- 014. Prepared by J. M; Omernik. E.P.A., Office of Research and
Development, Corvallis, OR. 106 pp.
U.S.EPA. 1992. Framework for Ecological Risk Assessment. Risk Assessment Forum. EPA 630/R-
92/001.
U.S. EPA 1993
U.S. Fish and Wildlife Service. 1995. Snake'River Aquatic Species Recovery Plan. 92pp.
Yearsley, J. R. 1991. A dynamic river basin water quality model. EPA Publ. #910/9-91-019. EPA
Region 10, Seattle, Washington. 22 pp.
. DRAFT—June 17.1996
43
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APPENDIX A:
PARTICIPANTS IN THE PROTECTION
OF THE MID-SNAKE RIVER
Federal
U.S. Environmental Protection Agency
(USEPA)
Department of the Interior.
' ' U.S. Fish and Wildlife Service
Bureau of Land Management/Minerals
Management Service
National Biological Survey
Department of Energy '
Federal Electric Regulatory
Commission
Department of Agriculture
National Park Service
U.S. Geologic Survey
Northwest Power Planning Council
State
Idaho .Department of Health and Welfare
Division of Environmental Quality
Idaho Department of Water Resources
Idaho Department of Fish and Game
Idaho Fish and Game Commission
Idaho Water Board
Idaho Department of Parks and Recreation
County/Local
Mid Snake River Planning Group
>
Private Organizations
Idaho Power Company
North Side Canal Company
The Nature Conservancy
Natural Heritage Program
The Research Community
The University of Idaho
Idaho State University
University of California at Irvine . .
44
Middle Snake River Watershed Ecological Risk Assessment
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APPENDIX B : REGULATORY (PART 1) AND NON-
REGULATORY (PART 2) FRAMEWORK
FEDERAL
U.S. Environmental Protection Agency
ripan Water Art (CWA)- National Pollutant nigfhargft F.ffliiftnt Permits"
The USEPA is responsible for the National Pollutant Discharge Elimination System (NPDES) program
In Idaho. The NPDES program provides for the issuance of permits for discharges and the
establishment of minimum treatment requirements as permit conditions. The Idaho Department of
Health and Welfare assists EPA in administering and enforcing the effluent discharge limitations and
issuing discharge permits for. waste discharges in the state. The point sources of greatest concern in
this study area include municipal facilities, fish hatcheries, and confined animal feeding operations
(primarily dairies and feedlots). .
Permits issued by EPA in 1990 include a provision that requires hatchery operators to monitor their
effluent for nutrients over a 1-year period. -Hatcheries have been, and will continue, monitoring
solids. These permits include a reopener clause that allows EPA^to modify permit requirements based.
on the results of this sampling effort. The Idaho Department of Health and Welfare, Division of
Environmental Quality (IDHW-DEQ) currently assists EPA in regulating hatchery effluents,
principally on the basis of suspended solids and biochemical oxygen demand loadings.
The IFSEPA has established regulations for waste disposal practices at stockyards and .feedlots.
Essentially, these regulations prohibit the discharge of animal wastes to streams and water bodies
except during particularly large runoff events. Even with these regulations, however, accidental or
illegal discharges of the wastes persist (M. McMasters, IDEQ, personal communication to P. Cirone,
1989). . '.'..'•
There is one municipal treatment facility in the Mid- Snake River Watershed at Twin Falls.
Sftgrinn 101 (H) Tntal Maximum Daily
Currently, nutrient management plans have been prepared to address CWA Section
303(d)requirements for development of total maximum daily loading for Billingsly Creek, and the
Snake River from Shoshone Falls to Lower Salmon Falls will be listed as water quality limited in the
next 305(b) report. The Sierra Club has filed an "Intent, to Sue" proceeding over the development of a
total maximum daily loading for this reach.
Federal Electric Regulatory Commission
Developers of proposed new hydroelectric projects in the Snake River are being asked to provide
environmental information about the impacts of the project at the site. In addition, they are required to
evaluate the cumulative impact of the proposed project on the system downstream from the site.
Relicensing of an existing hydroelectric facility raises issues different from those raised in the, licensing
of a new project. In most instances, older hydroelectric facilities coming up for relicensing were
constructed with little or no regard for environmental values. Relicensing provides an opportunity to
. ... . -*•
DRAFT— June 17, 1996 ' ' 45
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conduct.a proper environmental review of a completed project and'to change its structure .or operation-
to protect, mitigate, and enhance environmental and recreational values. Some relatively common \
relicensing requirements that benefit fisheries include the installation of fish.passage facilities,' or new '•
controls on the amount and timing of flow releases below a dam, so that dewatered stretches of river
"can once again be productive (Echeverria etal., 1989). :
The comprehensive water block arid target flow concept developed by the Federal Electric Regulatory
Commission will be explored in conjunction with the licensing and relicensing of hydroelectric
projects. Opportunities to increase flows in the reach of concern will be explored with the Department
.of Water Resources through the Upper Snake River Water Bank. Other alternatives for increasing
flow in the river will be developed as the opportunity arises. .
U. S. Army Corps of Engineers
The Corps of Engineers has primary responsibility for wetlands protection and permitting.
£7.5". Geological Survey ,
U. S. Fish and Wildlife Service .
STATE ' . ' - . ' . ."'•'•• -..'• • • :.
Idaho Division of Health and Welfare - Department of
Environmental Quality
State. Water Quality Tritftria > *
Under the CWA, Section 401 certification provides that federally permitted and licensed water-related
activities meet water quality standards established under the act. Unacceptable impacts that cannot be
adequately mitigated will result in denial of 401 certification for the project.
The general water quality criteria state that "waters of the state must not contain floating, suspended,
or submerged matter of any kind in concentrations causing nuisance or objectionable conditions of that
may adversely affect designated beneficial uses" (IDAPA 16.01.2200,04).
The general water quality criteria further state that "waters of the state must not contain . . . excess
nutrients that can cause visible slime growths or other nuisance aquatic growths impairing designated
or protected beneficial uses" (IDAPA 16.01.2200,05). Specific water quality criteria for waters
designated for cold-water biota must exhibit "dissolved oxygen concentrations exceeding 6 mg/1 at all
times" (IDAPA 16.01.2250,04.3). ' .
According to state law, the designated uses of the Snake River from_Milner Dam to King Hill are
listed as agricultural water supplyj cold water biota, salmonidspawning, and'primary and secondary
contact recreation (fishing, boating and swimming). .'
Beneficial uses found to be potentially at risk by the most recent nonpoint source assessment are
agricultural water supply and secondary contact recreation. Beneficial uses that are inadequately
supported include cold-water biota, salmohid spawning, and primary contact recreation. The primary
46 Middle Snake River Watershed 'Ecological Risk Assessment
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pollutants are sediment, nutrients, bacteria, and ammonia from agricultural activities, as well as flow
alteration from hydrologic/habitat modifications (IDHW, 1989). '•
State of Idaho Nutrient Management Act • • '
The Idaho Division of Environmental Quality (IDEQ) addresses nutrient (nitrate'and phosphate
pollution) concerns through the development and implementation of a nutrient management plan for the
basin, under the authorities of the State Nutrient Management Act. The objective of the act is the
formulation and adoption of a comprehensive state nutrient management plan through the development
of individual basin plans. The plan must identify nutrient sources, dynamics, and preventive or
remedial actions to protect surface waters.
As part of this effort the Mid-Snake River Nutrient Management Planning Group, consisting of two
•committees, has been formed:
- Executive Committee, a public advisory committee with representatives from canal
companies, the Mid-Snake Study Group, Hagerman Valley Citizen's Alert, Inc., food
processors, Idaho Conservation League, aquaculture, dairy/feedlot industry, Soil
Conservation Districts, municipal discharges, hydroelectric facilities, and Idaho
' Rivers United, and
»• Technical Advisory Committee, which, in addition to members of the Executive
Committee, includes the Water Quality Modeling Group and scientists with
appropriate expertise from several universities.
Wetlands Protection Grant
• Development of a 401 certification process with a wetlands protection grant from EPA will allow
formal consideration of wetland impacts.
Idaho Department of Water Resources . ,
%. '
Idaho Division of Fish and Game
LOCAL ;
Counties •
Counties in the area have enacted ordinances designed to protect the Snake River Canyon and water
quality, and there are a number of proposed or existing regulations that influence water quality. Twin
Falls County zones land within the canyon for outdoor recreation, and all but industrial or commercial
development is permitted in this zone. The plan encourages development and enhancement of
recreational opportunities in the Snake River Canyon (Twin Falls County Planning Department, 1987).
The county requires a 30:5 meter building setback from the canyon rim unless an engineer certifies
that the rim is stable; with certification, a 9.1 meters setback is allowed.
Jerome County has established a preservation zone along the north side of the Snake River Canyon.
This preservation zone generally extends from the river to 0.5 mile north of the river for public lands.
DRAFT—Jung 17. 1996 > .47
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Caldron Linn, Milner Dam reservoir, and the Snake River Canyon are included in the preservation •
zone'.' Lands'in this zone are to be preserved in their natural state for future public access (Jerome
County Planning Department, 1984). Present building regulations require a 30.5 meter scenic setback
from the canyon rim, and activities within the canyon are closely regulated. The "Jerome
Comprehensive Plan includes a provision for conserving surface water for irrigation, recreation, and
wildlife usesl
Jerome County is in the process of developing a Livestock Confinement Ordinance that will establish a
twofold permit process. If livestock concentrations are greater than five animal units per acre, the
landowner is required to obtain a permit. In addition, if the activity is located within 0.4km of a
stream drainage or in a ground-water area with a soils capability rating of "severe," the landowner is
required to notify adjacent landowners, the Soil Conservation Service, EPA, the Department of Water
Resources, and die Department of Health and Welfare. A public hearing will be held prior to issuance
of *a permit. *
NON REGULATORY ACTIVITIES
Mid-Snake River Planning Group
A regional planning group was organized in spring 1990 by the four counties in the Mid-Snake area—
Gooding, Twin Falls, Lincoln, and Jerome. The group also includes local sjate and federal agency
representatives in a nonvoting capacity. .The purpose of the Mid-Snake River Planning Group is
sustaining the economic activity of the region and development of a management plan to prioritize
problems in the basin and to provide direction for solving them. The primary focus of the plan is the
protection and enhancement of water quality in the Snake River. The plan was completed in Spring
1992. The group is serving as the policy advisory committee for development of a Mid- Snake River
nutrient management plan.
Water Qualify Modeling Group
A Memorandum of Understanding (MOU) has been developed among the state and federal agencies
with management concerns related to the Mid- Snake River. This MOU will facilitate the development
and use of a water quality model originally developed by EPA. ..,-',
Idaho Department of Water Resources/State Water Plan Activities . . '
As a result of the Idaho Department of Water Resources' planning efforts, a portion of the Snake .
River has been granted interim protected status by the Idaho Water Resources Bloard. (Subject to
legislative approval, the Board has the authority to designate protected rivers, thereby prohibiting
certain activities within the stream bed.)
The purpose of this authority is that "selected rivers possessing outstanding fish and wildlife,
recreational, aesthetic, historic, cultural, natural or geologic values should be protected for the public
benefit and enjoyment," Pursuant to section 42-1734D, Idaho Code, the Snake River, from Section 5,
Township 11 South, Range 20 East, B.M. to King Hill is under interim protected status for 2 years
(1991-1993). [It's 1996-this needs to be updated]
Once a waterway has been designated as an interim protected river, the Board is required to prepare, a
comprehensive state water plan for the .waterway. According to Frank Sherman, chief planner, "The
single overriding consideration in developing a comprehensive water plan for. this reach of river will
,< . ' '. "
48 ' Middle Snake River Watershed Ecological Risk Assessment
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be water quality." After the completion of the reach plan, the Water Resources Board will hold a'
public meeting to determine whether this stretch of river or a portion of it should be given permanent
protected status. As set out in Idaho Code 42-1734A, with this designation the Board can'prohibit
certain activities within the streambed: -
, > Construction or expansion of dams or impoundments
»• Construction of hydropower projects
»• Construction of water diversion works
»• Dredge or placer mining
»• Alterations of the streambed
. «
>• Mineral or sand and gravel extraction within the streambed.
Agriculture Projects . • , . '
An important component of the Nonpoint Source (NFS) Program jn Idaho is the State Agriculture
Water Quality Program. The State Agriculture Water Quality Program and the Idaho Agricultural ,
Pollution Abatement Plan (1983) have been developed to address nonpoint pollution that originates on ,
agricultural lands. The State Agriculture Water Quality Program, created in 1980, makes grants to
Soil Conservation Districts to assist in the development of water quality plans and to provide cost-
sharing with farmers who apply best management practices. The State Agriculture Water Quality
Program projects are funded with dollars from the Water Pollution Control Fund and are intended to
be demonstration projects that encourage farmers to adopt best management practices. Projects are
selected based on their water quality benefits. In the Mid- Snake River area, there are currently three
agricultural water quality projects funded under the State Agriculture Water Quality Program—Cedar
Draw, Vineyard Creek, and East Upper Deep Creek (planning only). Knowledge of the relative
contaminant contribution of the agricultural lands in the basin will enable IDEQ, in conjunction with
the Soil Conservation Districts and the Soil Conservation Commission, to prioritize watersheds in this
area. State Agriculture Water Quality Program funds can then be targeted to those areas contributing
the greatest load to the Snake River. •
The Idaho Division of Environmental Quality will perform consistency reviews of resource
management plans as they are developed for BLM districts in the area. This will ensure that the
permitted land use activities are conducted using appropriate best management practices to protect
water quality. • . .
National Rural Clean Water Program on Rock Creek
The Rock Creek project, federally funded by the National Rural.Clean Water Program, is a long-term
monitoring and evaluation project to p'rovide information and experience in controlling agricultural
nonpoint pollution. Federal programs such as the Rural'Clean Water Program have attempted to
improve water quality, largely by controlling sediment loads in agricultural irrigation runoff. Soil
erosion control programs have been instituted by the Soil Conservation Service and other agencies in
many of the Snake River's tributaries. A wealth of information on soil loss, erosion control, and the
effectiveness of best management practices has been collected as part of the Rock Creek Rural Clean,
DRAFT-Juiie-17, 1996 49
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Water Program.- Turbidity and sediment loads have been reduced in the Rock Creek watershed, and •
fish kills in the mainstem Snake River appear to have been eliminated within the study area (IDHW-'.
DEQ-WQB, 1989; W. Poole, personal communication to P. Cirone, 1989)! -
Idaho^Power . • ,
Environmental studies have been undertaken by-Idaho Power and federal and state agencies associated
with the relicensihg of severalldaho Power projects.
Idaho Department of Fish and Game "
Preservation of game species.
The Canal Companies
Diversion practices for irrigation needs. .
National Park Service •.-.•.,-
The Hagerman Fossil Bed National Monument abuts the reach. The Hagerman Reach was identified
as a potential Wild and Scenic River.
Northwest Power Planning Council , " . 0
The Mid-Snake River is a "protected area" in the NPPC habitat Plan.
Idaho Department of Parks and Recreation •
Malad Gorge State Park, Mokey P? State Park and. other instream flow concerns.
Bureau of Land Management
Resource Management Plans for Bureau of Land Management districts adjacent to the river.
The Nature Conservancy • • •
50 , '- Middle Snake'River Watershed Ecological Risk Assessment
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APPENDIX C: ECOLOGICAL COMPONENTS OF MJD-
SNAKE RIVER ECOSYSTEM
Aquatic and shoreline vegetation of the Snake River (Stanford 1942).
(Asterisks indicate common species)
Wetland plants .
*SaIixlasiandra tenth.
*Populus trichocarpa Torr. & Gray
*Nepeta cataria L.
*Solanum triflorum Nutt.
Veronica americana L.
Solidago missouriensis Nutt
Rumex persicaroides L.\ ' ^ •
Yicia americana Muhl.
Gfychrrizia lepidota Pursch
Apocynum cannabinum L. •
Verbena hastata L. , ,••-.*--
Mentha arvensis L. var Lanta Piper
Helenium autumnale L.
Xanthium pennsylvanicum Wallr.
Bidens cemua L.
' Artemisia sp.
' Sarcobatus sp.'
Phragmites communis trin.
Paspalum distichum L.
Polypogon montspelliensis L.
Cyperus strigosus L.
Eleocharis paliilsiris L.
Scirpus validus Vahl
Typha latifolla L. .
Pofygonon natans A. Eaton
Polygonon lapathifolium L. .
Sagittaria
Potamogeton epihydrous
Potamegeton pectinatus
Ceratophpyllum demersum
•Rorippa nasturtium L.
Anacharis
Lemna minor
Azolld '
Tpxicodendron diversiloba (Ton. & Gray) Greene
Additions from 1992 observations (Dey and Minshall 1992)
DRAFT—June 17, 1996
51
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Potomogeton crispus ." " :
Potomogeton foliosus
Elodea nuttali
Elodea canadensis ' '
Ranunculus spp.
Meriophyllum spicatum , '
Other plants found in the area include (Draft Nutrient Management Plan, 1994):
willow
cottonwood .,
. juniper _,-',.'
water birch -
netleaf hackberry
russian olive (introduced) • ...
chokecherry •
black locust ' . ,
squabush
golden current
dOgWOOd ••••;..-• . ° ; •••- : -"
wood's rose ,
nettle.
Solomon's seal
Some of the animals identified in the riparian areas include (Jdaho DEQ Nutrient Management
Plan, 1994):
mule deer
cottontail
shrew deer mouse
coyote ,
bobcat . .
muskrat • •
mink
warsel
otter ' . ,
raccoon
jackrabbit . •
marmot . .
, pygmy rabbit
badger
52 '--•,. . ' Middle Snake River Watershed Ecological Risk Assessment
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Amphibians and reptiles identified in the riparian areas include (Idaho DEQ Nutrient
Managment Plan, 1994):
sideblotched lizard
western whiptail
westernfence lizard
gopher snake
rubber boa
western rattlesnake . ,
Fish species in Mid-Snake River between King Hill and Milner Dam (personal communication,
Idaho Dept of Fish and Game 1993 and Idaho DEQ draft Nutrient Management Plan, 1994, Dey
and MinshaU, 1992)
Family: Acipenseridae - Sturgeons
'•->4<5 Acipenser transmontanus
Family: Salmonidae - Trouts
Cutthroat trout
Rainbow trout
Redband trout
Mountain whilefish
White Sturgeon
lOncorhynchus clarki
^Oncorhynchus mykiss
6Oncorhynchus mykiss gairdneri
^Prosophan williamsonil
**Salmo trutta
Family: Cyprinidae - Carps & Minnows
^Cyprinus carpio
sPtychocheilus oregonensis
5Mylocheilus caurinus
5Acrocheilus alutaceus
*Richardsonius balteatus
sRhinichthys osculus
*Gila atraria
5Rhinichthys cataractae
5Rhinichthys folcatus
Family: Catostomidae - Suckers
*Catostomus columbianus
sCatostomus macrocheilus
*Catostomus platyrhynchus
7Catostomus ardens
Family: Ictaluridae - Bullhead catfish
l-2MIctalurus punctatus
J*Ameiurus nebulosus
*-5Ameiurus melas
Brown trout
Common Carp
Northern squawfish
.Peamouth
Chiselmouth
Redside shiner
Speckled dace
Utah chub
Longnose dace *
Leopard dace
Bridgelip sucker
Largescale sucker
Mountain sucker
Utah sucker
Channel Catfish
Brown bullhead
Black bullhead
DRAFT—June 17, 1996
53
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Family: Centrarchidae - Sunfishes '•
l"3-5Micropterus dolomieu Smallmouth bass
^Micropterus salmoides Largemouth bass
^Lepomis gibbosus Pumpkinseed
3-5Pomoxisnigromacuiatus . Black crappie
3'5Lepomis macrochirus Bluegill
Family: Percidae - Perches •
^Percaflavescens • ' Yellow perch
™Stizostedion vitreum • . Walleye
Family: Cottidae - Sculpins
5Conusbairdi Mottled sculpin
greenei Shoshone sculpin
sCottus beldingi , Paiute Sculpin
5Cottus confitsus . Shorthead sculpin
5Cottus rhotheus Torrent sculpin -
Family: Sciaenidae -Drums . ' .
3'sAplodinotus grunniens1 . Freshwater drum
1 Game fish in the Mid-Snake River (IDEQ Nutrient Management Plan, r994)
2 Spawning fish (IDEQ Nutrient Management Plan, 1994)
Non-native species. Five additional non-native species likely present are:
Tilapia mossambica, T. Zellei, T. nilotica fthe Mozambique, Redbelly and Nile Tilapias,
respectively^, Lepomis cyanellus, and L. microlopKus (Green and
Redear sunfishes). -
4Considered a Species of Special Concern by the State of Idaho. N
5 Fish fauna of the Snake River drainage below Shoshone Falls (Bowler, et al. 1992 and Bowler and
Frest 1992). , ' . „ •
6 The only pure surviving population of Redband trout is in King Hill Creek; hybrids are found in
other tributaries.
7 Federal Energy Regulatory Commission, 1990 (FEIS for the Milner, Twin Falls, Auger Falls, and
Star Falls hydroelectric projects in Idaho, FERC/EIS-0048F).
Middle Snake River Watershed Ecological Risk Assessment
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Native fish species no longer present in the Mid-Snake River include Onchorhynchus tshawystcha,.
Chinook salmon, O. kisutch, Coho salmon, the anadroumous form of O. mykiss, Steelhead trour,. and.
Lampetra tridentaia, the Pacific lamprey.
Class Gastrioida (Snails)
26 Native . "
2 Exotic (non-native)
Ancylidae
Bulinidae
Hydrobiidae
Fluminicola columbiana ,..-'.
candidate endangered, cold water .
Potamopyrgus antipodarum • .
non-native)
Pyrgulopisis idahoensis
endemic to Mid-Snake and Lake Idaho, endangered, cold water '
Preferred habitat: sediment, beneath rocks . .
Bliss Rapids Snail • •
endemic to Mid-Snake and Lake Idaho, endangered,, cold, fast flowing water :
Lancidae
Fisherola nuttalli •
candidate endangered, cold water .
Lanxsp.
endangered, cold water :
Lymnaeidae
Radix auricularta
non-native
Physidae . .
Physa natriclna
endangered, cold water ,
Planorbidae '. • '
Valvatidae . ' •
Valvata utahensis . .
endangered, cold water •
Class Pelecypoda (Clams)
17 Native - • . ...
Candidate or Proposed Endangered
1 Exotic (non-native)
Corbiculidae
Corbiculafluminea. , .
non-native ;
Margaritiferida . .
Sphaeriidae
Unionidae ,
» * • -^
DRAFT—June 17, 1996 • ' .55
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Anodonta Califomiensis (California Floater)
candidate endangered, cold water . •
Inveriebrates identified as part of kick samples collected during September 1992 (Minshall and
Robertson 1992).
AUGER FALLS
Turbellaria (abundant)
Baetis tricaudatus (abundant) . •
Potamopyrgus (abundant snail)
, Prosirnulium (abundant)
Hydropsyche L
Hydroptila
Musculium (abundant clam)
Chironomidae , ,
Oligochaeta •
KANAKA RAPIDS
Coenagrionidae . •-*.,-:_' -.
Turbellaria . :
Baetis tricaudatus (abundant)
Potamopyrgus (abundant snail)
Hydropsyche . .' ••. '.
Hydroptila (abundant)
Ostracoda
Chironomidae (abundant) .
Oligochaeta
Simulium ••..•••"•-
Amiocentrus . '
Helicopsyche (abundant) . .
Rhycophila vaccua • .
Hydracarina .
POOL UPSTREAM OF KANAKA RAPIDS
Glossophinia (leech) . .
Piscicolidae (leech) , .
Caecidotea (Isopoda) " ,
Potamopyrgus (abundant snail)
Chironomidae (abundant)
Oligochaeta • '
Anodonta (mussel) .
56 . Middle Snake River Watershed Ecological Risk Assessment
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