An Interactive Guide to Nonpoint Source Monitoring

508-compliant content
U.S. Environmental Protection Agency (EPA)

EPA 841-B-22-001
February 2022

1. INTRODUCTION

1.1	The Guide's Target Audience

This guide is primarily for those who develop and implement monitoring plans for watershed
projects, but it can also be used by those wishing to evaluate the technical merits of
nonpoint source (NPS) pollution monitoring proposals they might sponsor.

Leveraging existing work from your group's strategy and monitoring documentation
(e.g., standard operating procedures, quality assurance project plans [QAPPs] with similar
objectives) will help you make the most of this interactive guide and develop an effective plan
for your project.

Note: If you are using Clean Water Act section 106 or 319(h) funds:

•	Review your monitoring approach to determine if it conforms to your state's/tribe's
water quality monitoring strategy.

•	Determine quality assurance needs early, including developing and approving a QAPP
before collecting any samples.

1.2	Why Do We Need Nonpoint Source Monitoring?

•	Identify water quality problems, designated use impairments and causes, and
pollutant sources.

•	Develop total maximum daily loads (TMDLs), including load and waste load
allocations.

•	Analyze trends.

•	Assess the effectiveness of best management practices (BMPs) or watershed projects.

•	Assess permit compliance.

•	Validate or calibrate models.

•	Conduct research.

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1.3	Fundamentals of Good Monitoring

•	Good monitoring

o Provides fundamental information about the water resource and its

impairments,
o Documents changes through time.

o Shows response to NPS pollution reduction practices and programs,
o Confirms achievement of management objectives,
o Provides basis for evaluating progress (adaptive management).

•	Poor monitoring

o Fails to meet objectives,
o Creates confusion,
o Leaves critical questions unanswered,
o Wastes time and money,
o Leads to bad decisions.

For more information, go to guidebook page 2-4.

1.4	This Interactive Guide Approach

•	This interactive guide offers a high-level overview of USEPA's NPS monitoring
guidebook, Monitoring and Evaluating Nonpoint Source Watershed Projects (referred
to in this document as the guidebook); it primarily focuses on Chapters 2 and 3.

•	By using the map on the next page, users may easily navigate directly to the details
that are most pertinent to their monitoring objectives.

For more information, go to guidebook page 2-4.

1.5	Quality Assurance Project Plan

•	Prepare your QAPP before data collection begins and refer to it during all phases of
the monitoring program.

•	A QAPP documents the planning, implementation and assessment procedures for a
particular project, as well as any specific quality assurance and quality control activities.

•	Use a QAPP to document planning results for environmental data operations and to
provide a project-specific "blueprint" for obtaining the type and quality of
environmental data needed for a specific decision or use.

•	For more on QAPPs, refer to the Design Data Management section or page 8-1 of the
Guidebook.

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2. MONITORING PLAN DESIGN ELEMENTS

• The following sections discuss monitoring plan design elements:

o	Identify Problems (Section 2.1)

o	Form Objective (Section 2.2)

o	Design Experiment (Section 2.3)

o	Select Scale (Section 2.4)

o	Determine Sampling Frequency (Section 2.5)

o	Locate stations (Section 2.6)

o	Choose Sample Type (Section 2.7)

o	Design Stations (Section 2.8)

o	Define Collection and Analysis Methods (Section 2.9)

o	Defined Land Use Monitoring (Section 2.10)

o	Design Data Management (Section 2.11)

IDENTIFY
PROBLEM(S)

LOCATE
STATIONS

DETERMINE

DESIGN I)	SAMPLING

EXPERIMENT/	FREQUENCY

9

9

determine; )

SAMPLING
FREQUENCY V

9	DESIGN

STATIONS ~

FORM _ ^	„	_

OBJECTIVES^^^^	W	O CH00SE

SAMPLE
TYPE

9

SELECT
VARIABLES

SELECT
SCALE

.9

DEFINE W	W DESIGN

COLLECTION T	~ DATA

& ANALYSIS	I 1	MANAGEMENT

METHODS	yf

DEFINE
LAND USE
MONITORING

2.1 Identify Problems

•	Identify the causes of impairment and the pollutant sources that need to be
controlled.

•	Considerations:

o How might the characteristics of your watershed affect water quality?
o How would you identify specific pollution problems?

2.1.1 Overview

•	Designing a monitoring program to assess response to NPS control programs requires
a thorough understanding of the system.

•	Questions that should be addressed during this step:

o What are the critical water quality impairments or threats?
o What are the key pollutants involved?
o What are the sources of these pollutants?

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o How are pollutants transported through the watershed?
o What are the most important drivers of pollutant generation and delivery?
o What are the areas that are ecologically or culturally significant, or critical, to
your community?

For more information, go to guidebook page 2-4.

2.1.2 Understand the System

•	Monitoring design influences:

o 2.1.2.1 Causes and sources of pollution
o 2.1.2.2 Pollutant transport
o 2.1.2.3 Seasonality
o 2.1.2.4 Water resource types
o 2.1.2.5 Climate

o 2.1.2.6 Soils, geology and topography
For more information, go to guidebook page 2-4.

2.1.2.1	Causes and Sources of Pollution

•	What, where and when should you sample?

•	Knowing the pollution source(s) allows you to apply the correct pollution control
measures and to monitor the watershed's response.

2.1.2.2	Pollutant Transport Considerations

•	How are pollutants transported from the source to the receiving water?

o Particulate pollutants (e.g., sediment) generally move in surface waters,
o Dissolved pollutants (e.g., nitrate-nitrogen) can be transported in both surface
and ground waters.

•	The distinct pollutant pathways need to be understood to decide where and when to
sample. (There might be pollutant sources upstream of your watershed.)

•	The timing of sampling during storm events can also be informed by knowledge of
pollutant pathways.

•	Monitoring for sediment or particulate phosphorus is often best focused on surface
runoff and streamflow.

•	In many cases, additional details regarding pollutant pathways must be understood to
fine-tune monitoring plans.

o Example: Monitoring decisions require an understanding of how pollutants move
through the system, such as whether to focus on high-flow events (e.g., for
particulate pollutants delivered episodically in surface runoff or storm flows) or
base flows (e.g., for dissolved pollutants that tend to be delivered continuously
via groundwater).

•	The timing of sampling during storm events can also be informed by knowledge of
pollutant pathways.

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For more information, go to guidebook page 2-5.

Agricultural runoff (photo by NRCS)

Field irrigation (photo by NRCS)

2.1.2.3 Seasonality Considerations

•	Seasonal patterns like snowmelt, rainfall, drought and humidity are often critical
factors in monitoring design because NPS pollution is highly weather-driven,

o In northern regions, snowmelt and spring rains are often the dominant

hydrologic feature of the annual cycle, and most of the annual pollutant load
could be delivered in a few weeks.

•	in cases where available water quality data are not sufficient to assess seasonality in a
specific watershed, it might be necessary to perform seasonal synoptic surveys, collect
year-round samples initially, or rely on watershed modeling to better define
seasonality and facilitate fine-tuning of the monitoring design.

•	Examples of seasonality:

o Seasonality Considerations —Example 1:

¦ February accounted for 23% of the total phosphorus (P) load in a 2-year
study in the Clear Lake watershed in Iowa, indicating that the snowmelt
period is a time of significant P loss from fields (Klatt et al. 2003).

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Iowa winter (photo by NRCS)

o Seasonality Considerations—Example 2:

¦ A 7-year study on corn-cropped watersheds in southwestern Iowa showed
that most of the average annual total nitrogen and phosphorus losses
occurred during the fertilizer application, seedbed preparation and crop
establishment period from April through June (Alberts et al. 1978).

Iowa cornfield (photo by Lynn Betts, NRCS)

o Seasonality Considerations—Example 3:

¦	For herbicides such as atrazine, losses from agricultural fields in humid
areas are highly episodic, with most of annual losses occurring in transient
storm events soon after herbicide application.

¦	A significant portion of the load of some pesticide degradation products,
however, can be transported under base-flow conditions in humid
environments.

•	Here, a monitoring effort would need to reliably monitor short,
intense and unpredictable events during specific seasons (depending
on seasonal & agronomic factors).

•	Sampling of base flow would be needed to track degradation
products.

For more information, go to guidebook page 2-6.

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Pesticide application (photo by C. Loper, USGS)

2,1.2.4 Water Resource Considerations

Waterbody type

Waterbody-specific considerations

Rivers and streams

Spatial flow patterns



Variability



Sampling selection

Lakes, reservoirs and ponds

Stratification



Shape



Flow patterns

Wetlands

Variability



Strategies and tools

Estuaries

Dynamics



Variability

Coastal nearshore waters

Dynamics



Variability

Groundwater

Variability



Sampling options

Water resource examples (photos by USEPA)

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2.1.2.4.1	Rivers and Streams

•	Spatial Flow Patterns

o Accurate flow measurement is essential to estimating pollutant loads. Therefore,
it's important to understand spatial flow patterns in the monitored stream or
river.

¦	Streams can be perennial or intermittent.

¦	Water velocity varies horizontally and vertically.

¦	Tributaries can add pollutant loads, dilute pollutant loads and create
horizontal gradients.

¦	Suspended solids, dissolved oxygen and algal productivity can vary with
depth.

•	Variability

o Vertical variability is particularly important during runoff events and in slow-
moving streams because pollutants can vary substantially with depth (Brakensiek
etal. 1979).

o Contaminant levels in bed sediment vary horizontally and vertically, as
deposition and scouring are strongly influenced by water velocity.

o Biological communities in stream systems vary with many factors, including
landscape position, type of substrate, light, water temperature, current velocity,
and amount and type of aquatic and riparian vegetation.

•	Sampling Selection

o If a representative sample of a river is required, it is important to select a
sampling point where the flow is uniform and well-mixed, without sharp flow
variations or distinct tributary inflow plumes.

o If more detail is required, segmentation of a stream into fairly homogeneous
segments before monitoring might be necessary, with one to several monitoring
stations located in each segment (Coffey et al. 1993).

2.1.2.4.2	Lakes, Reservoirs, and Ponds

•	Stratification

o The physical, chemical and biological characteristics of lakes vary horizontally,
vertically, seasonally and throughout the day.

o These characteristics are strongly determined by hydrology and geomorphology
(Wetzel 1975).

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EHUMMION OR MIXED LAYER - WARM (LIGHT) VWTER

THERMOCLINE

METALIMNION

DISSOL
OXYQEN

:-ri

"i'j* . r j- ¦

DISSOL
OXYGEN

HYPOUMNlON
COOL {HEAVY!- WATER

TEMPERATURE
PROFILE

Thermally stratified lake in mid-summer (image by USEPA 1990)

*	Shape

o Lake shape has major implications for monitoring design.

¦	Simple, rounded shapes tend to be well-mixed at most times and might
require only a single sampling station to provide an accurate
representation of water quality,

¦	Complex interconnected basins or dendritic shapes (e.g., reservoirs) tend
to exhibit significant spatial variability as mixing is inhibited; such lakes may
require numerous sampling stations to represent the more uneven water
quality characteristics.

•	Flow

o Vertical variability can affect water quality and consequently monitoring design
choices,

¦	Uniformly shallow lakes tend to be well-mixed vertically and have extensive
photic zones, yielding a fairly homogeneous water column that can be
effectively sampled at a single depth,

¦	Deeper lakes tend to stratify seasonally because of the temperature-
density properties of water.

¦	Monitoring at different points with depth during periods of peak
stratification is sometimes appropriate. Other times, sampling during the
periods when the water column is completely mixed (e.g., at spring or fall
turnover) may yield information on the general character of the lake for
that year.

o Tributary inflows and effluent discharge points contribute to horizontal
variations in water quality.

¦	Localized inputs of large water or pollutant loads can influence localized
water quality. Currents influence the dispersal of pollutants.

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¦	Locations of such discharges are key factors in placing monitoring
stations—either to deliberately sample them to represent important
localized impairments or distinct components of total lake inputs, or to
deliberately avoid them as unrepresentative of the broad lake, depending
on program objectives.

o Sediment/water interactions exert strong controls on some pollutant dynamics.

2.1.2.4.3	Wetlands

•	Variability

o Due to the diversity among natural wetlands, a wetland monitoring program

must be based on a specific wetland's attributes,
o Key consideration for wetlands monitoring: define the assessment area (i.e., is it

the entire wetland or just a portion?)
o Wetlands cycle sediments, nutrients and other pollutants vary actively among
physical (e.g., sediment), chemical (e.g., water column) and biological (e.g.,
vegetation) compartments,
o Vegetation is a key element of wetland systems (seasonality of vegetation
growth and senescence may be an important driver for nutrient cycling) and
therefore important for monitoring design (USEPA 2002).

•	Strategies and Tools

o Strategies for designing an effective monitoring program build from a hierarchy
of three levels that vary in intensity and scale:

¦	Level 1: Broad, landscape-scale assessments.

¦	Level 2: Rapid field methods.

¦	Level 3: Intensive biological and physio-chemical measures (USEPA 2004).
o Rapid assessment procedures are sensitive tools to assess anthropogenic

impacts to wetland ecosystems; they can be used to:

¦	Evaluate best management practices.

¦	Assess restoration and mitigation projects.

¦	Prioritize wetland-related resource management decisions.

¦	Establish aquatic life use standards for wetlands.

2.1.2.4.4	Estuaries

•	Dynamics

o Estuaries differ from freshwater bodies largely due to the mixing of fresh water
with salt water and the influence of tides on the spatial and temporal variability
of chemical, physical, and biological characteristics.

¦	Incoming tides push salt water shoreward.

¦	Outgoing tides pull water toward the ocean and freshwater fills the gap left
by the receding submerged salt water.

¦	Because of the dynamic interaction of fresh water and salt water,
pollutants in the water and sediment remain in the estuary for a long time.

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River

Ocean 	»-

""	 " " ' 	 "	

Fresh Water





» —-1	1



if 			





Sediment



Mixing of salt and fresh water in an estuary (Chesapeake Bay Program 1995)

•	Variability

o Basin shape, mouth width, depth, area, tidal range, surrounding topography and
regional climate all help to determine the nature of an estuary.

o The earth's rotation, barometric pressure and bathymetry affect circulation and
spatial variability.

o Freshwater inflow is a major determinant of the physical, chemical and biological
characteristics.

¦	Freshwater inputs can vary seasonally and affect the concentration and
retention of pollutants, the distribution of salinity, and the stratification of
fresh water and salt water,

o Temporal variability is also influenced by factors other than freshwater inputs.

¦	Temperature profiles vary seasonally

¦	Tidal cycles can affect the mixing of fresh and salt waters and the position
of the fresh water-salt water interface.

2.1.2.4.5 Coastal Nearshore Waters

•	Dynamics

o Nearshore waters include an indefinite zone extending away from shore, beyond
the breaker zone; the term applies to both coastal waters and large freshwater
bodies such as the Great Lakes.

o The interplay of wind, waves, currents, tides, upwelling, tributaries and human
activities influence water quality and monitoring requirements.

¦	Wind and tides are the primary sources of energy.

¦	Waves play a central role in the transport and deposition of coastal
sediments as well as the dispersion of pollutants and nutrients.

•	Variability

o Upwelling brings cold, nutrient-rich waters to the surface, encouraging biological
growth.

¦	Extremely variable in space and time, depending on winds and topography.

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o Tributaries introduce fresh water and can alter nearshore currents depending on
tide stage, wind conditions, and flow rate.

¦	Headlands, breakwaters, and piers can affect the circulation pattern and
alter the direction of nearshore currents.

¦	Current patterns must be sufficiently understood to determine the best
locations for monitoring and to establish pollutant pathways and the likely
relationships between land-based activities and nearshore water quality.

¦	Because circulation and pollutant transport is so variable in nearshore
areas, designing monitoring plans based on assumptions about current
patterns is not recommended.

¦	The current system drives the relationship between land-based pollutant
sources and receiving water quality.

•	Monitoring should include provisions to track variables needed to
characterize the current enough to aid interpretation of other
chemical, biological, and physical data that are generated.

•	Basic data on salinity, water temperature, and depth are often
essential to identifying the source of the sampled water and
characterizing current patterns.

2.1.2.4.6 Groundwater

•	Variability

o Occurs in either confined or unconfined aquifers.

o Water quality is influenced by aquifer type, native geology, precipitation
patterns, flow patterns, land use, pollutant sources, and pollutant
characteristics.

o The interaction of surface water and groundwater can be considered from the
perspective of:

¦	Surface water recharging groundwater, which is important when
determining the impact of surface water on a groundwater resource.

¦	Groundwater discharging to a stream or lake, which should be a key
element of monitoring when groundwater comprises a significant portion
of the water or contaminant budget of a surface water body.

o Karst systems (a geologic condition shaped by the dissolution of channels or
layers of soluble bedrock due to the movement of water) present special
challenges because sources of aquifer contamination may be widely dispersed
and difficult to map.

•	Sampling

o Regional or statewide groundwater level recording and water quality monitoring
networks are common across the nation, especially in areas where groundwater
is a primary source of drinking and irrigation water.

¦	These networks often detect contaminants via well monitoring and model
contaminant transport based on groundwater level data.

¦	Watershed-level monitoring of groundwater is still relatively rare.

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o Successful monitoring design begins with an understanding of the groundwater

system and the establishment of specific monitoring objectives,
o Monitoring often requires a two-stage approach;

¦	First stage is a hydrogeologic survey.

¦	Second stage is an investigation of water quality.

Artesian well in Sycamore Valley, MO (photo by J. Baughn, USGS)

2.1.2.5 Climate Considerations

•	What is the expected range of climate conditions? Note: Climate change is discussed
in future sections

•	The frequency, intensity and duration of runoff-producing storm events affect:

o Sampling frequency and duration
o Equipment selection
o Automatic sampler programming
o Many other elements of a monitoring program

For more information, go to guidebook page 2-21.

Photo by USEPA

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Photo by USEPA

Photo by Tetra Tech

2.1.2.6 Soils, Geology and Topography

•	What are the soil and substrate like? Is the area flat or sloped?

•	Soil, geology, and topography influence the hydrologic budget, pollution sources and
loading, and other factors that drive monitoring program design.

o Soil groups affect runoff and pollutant yields.

o Geomorphology and substrate geology determine riparian zone function and
pollutant delivery to nearby waters.

o Slope must be factored into the monitoring design:

¦	Height and slope length affect (1) the rate and duration of runoff from a
watershed, (2) rate of erosion, (3) depth of soil, and (4) stream
characteristics.

¦	Slope influences the likelihood of landslides and debris flow, erosional
processes and weathering rates.

For more information, go to guidebook page 2-22.

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Soil types may vary across the landscape (photos by NRCS)

2.1.3 Identify Problem(s)—Summary

•	Have you completed the following?

o	Identified the critical water quality impairments or threats

o	identified the key pollutants

o	Identified the sources of the key pollutants

o	Identified methods of pollutant transport

o	Identified the most important drivers of pollutant generation and delivery

2.2 Form Objectives

•	Formulating clear monitoring objectives is an essential first step in developing an
efficient and effective monitoring plan.

•	Considerations:

o What questions do you want to answer?
o How do your objectives fit into your overall program?

2.2.1 Overview

•	Well-formulated monitoring objectives drive the rest of the monitoring study design
and are critical to a successful monitoring project.

•	NPS monitoring data can be used to:

o Identify water quality problems, use impairments and causes, and pollutant
sources

o Develop TMDLs and load or wasteload allocations
o Analyze trends

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o	Assess the effectiveness of BMPs or watershed projects

o	Assess permit compliance

o	Validate or calibrate models

o	Conduct research

2.2.2 Monitoring Objectives

•	Questions that a monitoring program can answer:

o Has a waterbody's condition changed over time?

o Is there an emerging problem area that needs additional regulatory and/or
nonregulatory actions to support water quality management decisions?

•	Example: Little Miami River, Ohio

o Each year Ohio EPA (OEPA 2021) collects data from streams and rivers in five to
seven different areas of the state. About 400-450 sampling sites are examined,
and each site is visited more than once per year,
o During these studies, technicians collect chemical samples, examine and count

fish and aquatic insects, and take measurements of the stream,
o There are three major objectives for the studies:

o Determine how the stream is doing compared to goals assigned in the Ohio

Water Quality standards;
o Determine if the goals assigned to the river or stream are appropriate and
attainable; and

o Determine if the stream's condition has changed since the last time the stream
was monitored.

Little Miami River, OH (photo by Ohio EPA)

2.2.3 Program Objectives

•	All monitoring programs should be designed to answer questions.

•	Monitoring objectives should be directly linked to overall program or project
objectives.

•	Note: You might need to adapt monitoring objectives based on available resources.

•	Program objectives should be linked to management decisions/actions.

•	At the start of the project, ensure necessary resources are available.

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Example program objective

Complementary monitoring objective

Reduce annual phosphorus loading to the lake by
at least 15% in 5 years using nutrient management.

Measure changes in annual phosphorus loading to the lake
and link the changes to management actions.

Reduce E. coli load to stream to meet water quality
standards within 3 years.

Measure changes in compliance with water quality
standards for E. coli.

2.2.4 Form Objectives—Summary

•	Have you formed your monitoring objectives?

•	Do your monitoring objectives fit into your overall program?

2.3 Design Experiment

•	Choose a monitoring design before monitoring begins to ensure you can collect the
data needed to best meet your objectives.

•	Considerations:

o Will your design generate the data you need?
o Is your design financially and technically feasible?

2.3.1	Overview

•	Your monitoring objectives will drive decisions about your monitoring program.

o Several experimental study designs can be applied to meet monitoring
objectives, and some of the choices are obvious.

•	Select a monitoring design that:

o Best matches available resources,
o Presents the fewest logistical obstacles.

2.3.2	Monitoring Design as a Function of Objective

For more information, go to guidebook page 2-44.

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Design options

Short description

Objectives

Problem
assessment

TMDL loads

Trends

BMP

effectiveness

Reconnaissance/
synoptic

Multiple sites distributed across study area; monitored for
short duration (<12 months)

X







Plot

Traditional research study design; BMPs replicated in
randomized block design







X

Paired

Treatment and control watersheds monitored during
control and treatment periods



X



X

Single watershed
before/after

Single station at study area outlet monitored before and
after BMP implementation



X

X



Single-station long-
term trend

Single station at study area outlet monitored before and
after BMP implementation



X

X



Above/below

Stations with paired sampling upstream and downstream
of BMP(s)

X

X



X

Side-by-side

Same as single watershed because there are no
calibrating paired samples



X

X



Multiple

Multiple watersheds monitored in two or more groups:
treatment and control







X

Input/output

Stations located at input and output of BMP







X

2.3.2.1 Reconnaissance or Synoptic Design
• Use to:

o Determine magnitude and extent of problem,
o Target critical areas,
o Obtain preliminary data where none exist.

For more information, go to guidebook page 2-34.

Reconnaissance or Synoptic

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2.3.2.2 Plot Design
• Use to:

o Assess soil conditions, including nutrient levels,
o Assess pollutant transport pathways,
o Determine the effects of BMPs on pollutant transport.

For more information, go to guidebook >age 2-35.

Plot Design

~ Treated
Area A

4 Monitoring i	1 Treated

Station |	1 Area B

2.3.2.3 Paired Design
• Use to compare data from two watersheds (treatment and control)
For more information, go to guidebook >age 2-36.

Paired Watersheds
Calibration Period	Treatment Period

2.3.2.4 Single Watershed Before/After Design

• Use to measure pollutant loads before and after implementation of the TMDL.
o A single monitoring station is located at the outlet of the study area,
o Sampling is performed before and after BMP implementation,
o This design is not recommended for BMP effectiveness studies because:
o There are no control stations (as in the paired design described earlier),
o BMP effectiveness cannot easily be distinguished from other confounding effects
(USDA-NRCS 2003). Example: If the "before" years are relatively dry and the "after"
years are relatively wet, the differences in water quality and loads could be due
to differences in weather rather than the effects of implemented BMPs.

For more information, go to guidebook >age 2-38.

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Single Watershed

Before	After

2.3.2.5 Single Station Long-Term Trend Design

• Use to determine changes in water quality or pollutant loads over time,
o Advantages:

¦	Single monitoring station

¦	Wide applicability

¦	Ability to account for lengthy lag times
o Challenges:

¦	Requires a long duration

For more information, go to guidebook lage 2-39.

2.3.2.6 Above/Below Design

• Use to compare data from above and below treatment area.

o Design stations are located upstream (or upgradient) and downstream (or down-
gradient) of the area or source that will be treated with BMPs.

For more information, go to guidebook >age 2-39.

Above Station

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2.3.2.7 Side-By-Side Before/After Design

• Use to monitor adjacent watersheds without calibrating paired samples before
treatment.

o Not recommended for evaluating BMPs or watershed projects
o Very likely you'll be unable to distinguish among causal factors such as BMPs or
land treatment, inherent watershed differences, or an interaction between
BMPs and watershed differences.

For more information, go to guidebook page 2-41.

Side-by-Side Watersheds

2.3.2.8 Multiple Watersheds Design

•	Use to estimate the variability in a large group of watersheds

o Requires that more than two watersheds are selected for monitoring within

geographic area of interest,
o Two different treatments, and sometimes a control, are replicated across the
monitored watersheds in roughly equal numbers.

•	Challenges:

o Often not a practical choice
o Several years of monitoring is often necessary
o Cost can be high

•	Example: Multiple watersheds

o Lewis (2006) describes a multiple-watershed approach in which:

¦	Three of 13 watersheds are used as controls

¦	Five are fully treated

¦	Five are partially treated

o He argues that this design has a significant advantage over paired-watershed
studies in that it allows for prediction under different conditions or treatment
levels, whereas prediction based on paired-watershed study results requires the
assumed treatments are identical to the treatments used in the study.

For more information, go to guidebook page 2-41.

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Multiple Watersheds

Control	Treated	Treated	Partially Treated

0' %

4 Monitoring Station ~ Treated Area 1 1 Partially Treated

2.3.2.9 Input/Output Design

•	Use to compare data from before and after water moves through a BMP,

For more information, go to guidebook jage 2-41.

Input/Output
InflowOutflow

^^0* ' ^

4 Monitoring Station Untreated Treated

2.3.3	Critical Areas

•	Data collected in the problem assessment phase can be used to help define critical
source areas for pollutants—this is key to understanding the watershed, prioritizing
land treatment, and evaluating project effectiveness. A critical source area is defined
as an area within a watershed that can contribute a disproportionately large amount
of pollution. Generally located where high-magnitude pollutant sources (e.g., eroding
hillsides) overlap or interact with land areas that have a high pollutant transport
potential (e.g., areas prone to generating high volumes of runoff).

•	Example: With concurrent data from monitored subwatersheds or tributaries, you can
use statistical tests to identify significant differences in pollutant concentration or load
among multiple sampling points. These data can be displayed graphically in a map to
show watershed regions that could be major contributors of pollutants.

For more information, go to guidebook page 7-42.

2.3.4	Design Experiment—Summary

•	Have you selected a design for your experiment?

o Reconnaissance is best for the assessment phase of a watershed project,
o Above/below monitoring can help provide information about an isolated source
or area.

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o Paired, above/below-before/after, plot and input/output designs are generally

best for evaluating the effectiveness of BMPs or watershed projects,
o The paired, single watershed before/after, single-station long-term trend,
above/below, side-by-side and multiple study designs can provide useful load
estimation in support of TMDLs if flow and relevant variables are monitored,
o Single-station long-term trend design is often used for trend detection at certain
points in time.

2.4 Select Scale

•	Determine the size of the area you will monitor.

•	Considerations:

o What are the objectives of your study?
o What resources are available to you?
o What is your timeframe?

2.4.1	Overview

•	The choice of scale affects monitoring costs, duration and logistics.

•	Questions to address during this step:

o	What is the study duration?

o	What type of water resource will be monitored?

o	How complex is the project?

o	What are the available resources?

2.4.2	Options for Scale Selection

Watershed

23


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BMP or practice

Note: The ability to isolate the factors of interest (e.g., BMP effectiveness, transport
pathways) generally increases as scale decreases, but the transferability of results
generally decreases as scale decreases.

For more information, go to guidebook page 2-29.

2.4.3 Summary of Scale Options

Choosing monitoring scale as a function of objective;

Monitoring scale

Objective

Problem
assessment

TMDL

loads

Trends

BMP

effectiveness

Watershed

project
evaluation

Statewide/regional

X









Watershed

X

X

X



X

BMP: Plot







X



BMP: Field

X

X



X



Note: Monitoring can be performed at scales ranging from national to single points, but
the primary options for the types of NPS monitoring studies addressed in detail by
LJSEPA's guidebook are the watershed and BMP scales, the latter of which includes plot-
scale and field-scale studies,

For more information, go to guidebook >age 2-29.

2.4.3.1 Statewide or Regional-Scale Monitoring

•	A statewide or regional-scale study generally emphasizes larger streams and rivers,
public lakes and watershed outlets.

•	Studies are typically designed to assess current conditions.

•	Monitoring is often done near USGS gauging sites to take advantage of flow data.

24


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•	Cost and logistical constraints limit most monitoring efforts to the collection of grab
samples, a few field measurements (e.g., temperature, dissolved oxygen,
conductivity), and biological and habitat monitoring.

•	Monitoring frequencies are generally low.

•	Trend analysis is difficult to perform.

For more information, go to guidebook page 2-29.

2.4.3.2	Watershed-Scale Monitoring

•	A key difference between watershed- and state-level monitoring is the narrowing of
focus and increased intensity of watershed-level monitoring.

•	Important questions to ask include:

o What are the study's specific objectives?
o What is the size of the watershed?
o What are the parameters of concern?

•	Initial efforts generally focus on refining the problem definition, including:

o Better characterizing the water quality problem
o Determining the major sources and causes of the problem
o Providing data to help design a plan to solve the problems

•	Monitoring during the pre-implementation phase of a watershed project may include:

o	A synoptic survey (see guidebook p. 2-34)

o	Tests for toxicity (see guidebook p. 3-84)

o	Flow measurements to support a load analysis (guidebook p. 3-10)

o	Detailed habitat assessments (see guidebook p. 3-27)

For more information, go to guidebook page 2-29.

2.4.3.3	BMP- or Practice-Scale Monitoring

•	Monitoring at this scale:

o Is typically the most intensive type.

o Ranges from plot-scale monitoring to larger, field-scale monitoring.

•	Questions to ask:

o What type of BMP is being used?
o What specific sources are being treated by the BMP?
o Is the monitoring only storm-event driven or does base flow need to be
considered?

o Is adequate funding available to support the higher cost of monitoring at the
BMP/practice scale?

For more information, go to guidebook page 2-31.

25


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*V. A

MD

~

VA



Forested





i:. 4



Treatment 'JP

\ t ' ' *



_ /

* : 1

V

11

a UrbarvControl



A

¦¦'JBHW



Clarksburg monitoring study: watershed types (image by USGS)

2.4.3.3.1	Plot-Scale Monitoring

•	Generally used in designs that feature replication (e.g., to meet research objectives).

•	Can be used for preliminary assessment of BMP effectiveness.

•	Focuses on storm events and generally requires:

o Automatic samplers
o Continuous flow measurement
o Considerable annual expense

2.4.3.3.2	Field-Scale Monitoring

•	Samples are taken from episodic runoff rather than from waterbodies.

•	Study units are larger than individual plots but vary in size, such as:

o	Parking lots

o	Rooftops

o	Street segments

o	Cropland segments

o	Paddocks

o	Barnyards

2.4.4 Selecting Scale—Summary

•	Have you selected the scale of your monitoring project that best meets your project
objectives?

•	Does the scale meet your budget and logistical constraints?

o Statewide or regional
o Watershed
o BMP or practice

¦	Plot

¦	Field

26


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2.5 Determine Sampling Frequency

•	Determine how often to collect samples and determine the duration of your sampling
program.

•	Considerations:

o	What types of waterbodies are involved?

o	What variables need to be measured?

o	What is the system's variability?

o	What is your budget?

2.5.1	Overview

•	This section covers two critical questions:

o How often to collect samples (what is the sampling frequency or interval
between samples)?

o How long to conduct a sampling program (what is the sampling duration)?

•	Decisions will depend on program objectives, type of water body involved, variables
measured and available budget.

•	Sampling frequency must be relatively high (e.g., daily to weekly) to evaluate
effectiveness of a single BMP or to document the mechanisms controlling water
quality at a particular site.

•	A program with an objective of detecting a long-term trend or evaluating watershed
program effectiveness can accept longer intervals (e.g., weekly to monthly) between
samples.

For more information, go to guidebook page 3-43.

2.5.2	Selecting a Sampling Interval

•	This schematic of sampling frequency as a function of system type offers a general
guide to the relationship between system variability and sampling interval.

For more information, go to guidebook page 3-43.

27


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Low

High

System Variability

(Source: USDA-NRCS 2003)

2.5.3	Calculating the Appropriate Frequency

•	Calculating the appropriate sampling frequency varies with the statistical objective for
the monitoring data and sampling regime.

•	The following slides provide examples of how sampling frequency in the context of
simple random sampling can be calculated for estimating the mean and detecting
trends.

For more information, go to guidebook page 3-43.

2.5.4	Estimating the Mean

•	Estimating the Mean—A common monitoring objective is to be able to estimate the
mean value of a water quality variable (with a specific level of confidence).

•	You can calculate the necessary sample size using this equation:

where:

n = the calculated sample size

t = Student's t at n-1 degrees of freedom and a specified confidence level
s = estimate of the sample standard deviation

d = acceptable difference of the estimate from the estimate of the true mean, or V* of
the confidence interval from the mean

For more information, go to guidebook page 3-44.

n =

28


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2.5.5 Detecting a Change or Trend

•	Another common monitoring objective is to detect a change or trend in the value of a
water quality variable (with a specific level of confidence).

•	Two types of change can occur in the water quality variable being studied:

o A step change that compares the pre- and post-water quality mean values

o A linear (gradual, consistent) trend over time

For more information, go to guidebook page 3-45.

Trend analysis can
answer questions like:

"Are streamflows
increasing as
urbanization increases f"
or

"Have nutrient

loads decreased since
the TMDL was
implemented?"

2.5.5.1	Detecting a Step Change

•	To determine the sample size needed to detect a step change, the detectable change
must first be calculated based on the standard deviation of the difference between
the pre- and post-mean values with an anticipated number of samples.

o See guidebook p. 3-50 for an example calculation

•	The sample size needed to detect a step change difference of acceptable magnitude can
be estimated using an iterative process of trying different pre- and post-sample sizes.

2.5.5.2	Detecting a Linear Change

•	Monitoring for trend detection must be sensitive enough to detect the level of water
quality change likely to occur in response to management changes.

•	For a linear trend, this monitoring is based on the confidence interval on the standard
deviation of the slope.

o For equations and calculations, see guidebook >. 3-45.

•	Calculate sample size interactively by trying various sample frequencies and durations
until your monitoring approach would be able to detect the amount of change
expected by implementing BMPs.

29


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2.5.6	Minimum Detectable Change (MDC)

•	MDC—the minimum change in a pollutant concentration (or load) during a given time
period required for the change to be considered statistically significant.

•	You can use the MDC to:

o Estimate the required sampling frequency based on the anticipated change in

pollutant concentration or load,
o Estimate the change in pollutant concentration or load needed for detection
with a monitoring design at a specified sampling frequency.

For more information, go to guidebook page 3-47.

Minimum, detectable change
analysis can answer questions like:

"How much change must be
measured in a water resource
to be considered statistically
significant?"
or

"Is the proposed monitoring plan
sufficient to detect the change in
concentration expected from BMP
implementation?"

2.5.7	Sampling Duration

•	A monitoring program should be conducted long enough to achieve objectives or
document a change.

•	Basic guidelines for choosing a sampling duration include:

o Capture at least one full cycle of natural or cultural variability (e.g., weather,

construction management)
o Use statistical tests to evaluate a monitoring period's adequacy
o Consider the lag time

For more information, go to guidebook page 3-56.

2.5.8	Lag Time

•	Lag time—the time elapsed between when you install/adopt management measures
at the level projected to reduce NPS pollution and when you see the first measurable
improvement in water quality in the target waterbody.

30


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•	Knowledge of key lag time factors can help determine the required duration of a
monitoring program.

o Example 1: If groundwater travel time from an agricultural field through a

riparian forest buffer to a stream is known to be 5 to 10 years, it's reasonable to
expect to continue monitoring at least that long,
o Example 2: A lake with a flushing rate of 1.5 years might respond much more
quickly to changes in pollutant inputs, so a shorter monitoring program could
suffice.

•	Components of lag time experienced in land treatment/water quality projects:

Planning and
implementation
process

Time required
for practiced)

to produce
desired effect

Time required
for effect to be

delivered to
water resource

Time required
for water body
to respond
to effect

f Measurement
I Components

For more information, go to guidebook »age 6-4.

2.5.9 Overcoming Limited Resources

•	Financial resources should not be the primary basis for deciding on sampling
frequency.

•	To achieve desired objectives when resources are limited, determine whether you

can:

o Reduce the list of variables analyzed
o Reduce the number of stations
o Use less expensive surrogate variables
o Simplify field instrumentation
o Take composite samples

•	Reminder: When developing your monitoring program objectives, ensure that
necessary resources are available.

31


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2.5.10 Determine Sampling Frequency—Summary

•	Have you determined the variability of your system?

•	Have you chosen your sampling frequency?

•	Have you chosen the duration of your project?

•	Have you factored in lag time?

•	Do you have the necessary resources?

2.6 Locate Stations

•	Choose the specific locations where you will collect samples.

•	Considerations:

o What is the waterbody type?

o Will samples represent the conditions being monitored?
o Are there logistical constraints?

2.6.1 Overview

• Monitoring station locations must be determined at two distinct scales:
o Macro-scale—sampling locations are determined by:

¦	Experimental design and monitoring objectives

¦	Waterbody type

o Micro-scale—sampling locations are determined by:

¦	Site accessibility

¦	Physical configuration

Fall River Watershed

(Image from USEPA 2012)

32


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(Image from Dressing 2018)

2.6.2 Macro-Scale Factors: Design and Objectives

• Reminder—Monitoring design and objectives will control station location and can
differ depending on waterbody type, (For more information, refer to the Monitoring
Design as a Function of Objective section).
o Reconnaissance or synoptic: Needs many stations located in places that can
isolate particular drainage areas or NPS pollutant source areas (an example is
provided below).

o Single watershed or trend: Requires that a station be located at a watershed

outlet to represent the entire drainage area,
o Above/below or input/output: Calls for two or more stations to bracket a
treated area or BMP to allow comparison of concentrations or loads entering
and leaving the area.

o Groundwater monitoring: Requires an extensive network of monitoring wells to
determine flow into and out of the area and to map the aquifer's hydrogeologic
properties.

For more information, go to guidebook page 3-38.

Example macro-scale design: Synoptic - possible sampling locations for a synoptic survey.

33


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2.6.3 Macro-Scale Factor: Waterbody Type

•	On streams or rivers, station locations might be selected to capture or avoid the
effects of tributary streams, to isolate subcatchments, or to focus on areas with
particular characteristics.

•	In lakes and reservoirs, monitoring stations at each major tributary discharge might be
required to measure load for a TMDL. Lake morphology, vertical stratification, and
currents might require samples in several lake regions and/or at several depths.

•	For groundwater systems, the location of stations is determined by aquifer type and
by vertical, horizontal, and longitudinal variability in both water quality and water
quantity.

For more information, go to guidebook page 3-38.

Natural Lake

Water Column Sampling
Locations

Impoundment

a Ground water aquifers

Land surface



. Water tabie'^v



Unconfned aquifer

	Stream





Impermeable layer

Confined aquifer

Bedrock



c Multilevel wells	yyg||

Sand-/
pac* -s

£
t

}

b Monitoring source areas

d Vertical locations

(Images from USDA 2003)

Wei Source

Perched
water table

		S\

i I I

1 1

	, ' 1 T

Clay

3'

Water table

Bedrock —			

34


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2.6.4	Micro-Scale Factors: General

•	Site should be representative of the conditions being monitored.

o What type of flow are you measuring?
o Are you collecting biological measurements?

•	Consider site accessibility and physical configuration. Site should:

o Be easily accessible
o Be safe for field staff

o Have available power and communication links

o Have permission granted from property owners and state or local transportation
agency

o Be secure from both human interference and natural threats (e.g., flooding)
For more information, go to guidebook page 3-41.

2.6.5	Micro-Scale Factors: Flow Measurement

•	Special consideration for locating stations when flow is measured in an open channel:

o Want:

¦	Select a reach that's unobstructed and straight, has a flat streambed, and is
located away from the influence of changes in channel width.

¦	Choose an area with a stable cross-section and where depth and velocity
measurements can be conducted safely at low flows.

¦	Seek an area where a bridge crossing or walkway allows safe velocity
measurements at high flows.

¦	Look for areas where the stage can be measured and/or recorded
continuously (e.g., a protected area for a staff gauge).

o Avoid:

¦	Avoid culverts, waterfalls and bridges where obstructions or degraded
structures could cause hydraulic anomalies.

¦	Avoid areas that are subject to frequent sediment deposition or severe
bank erosion.

•	When flow is measured at an edge using a weir or flume, look for sites where:

o Flow can be collected and/or diverted into the device,
o Ponding caused by a weir will not cause problems,
o Any concentrated discharge from a flume can be safely conveyed away
downstream.

For more information, go to guidebook page 3-42.

35


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120- V-notch weir, Englesby Brook, Burlington, VT (USEPA 2016)

2.6.5 Micro-Scale Factors: Biological Monitoring

• Several important considerations for locating biomonitoring sites are:
o Ensure a comparable habitat at each station.

o Avoid locally modified sites unless project objectives include assessing their
effects.

o Avoid sampling near the mouths of tributaries entering large waterbodies (these

will not be representative of the entire waterbody).
o Include a reference site to provide data on the best attainable biological
conditions in a local or regional system of comparable habitat.

For more information, go to guidebook page 3-43.

Field processing offish sample: taxonomic identification and data recording (USEPA 2016)

2.6.6 Locate Stations—Summary

• Have you selected the location for your monitoring stations based on both the macro-
scale and micro-scale?
o Macro-scale: sampling locations must be determined by experimental design,
monitoring objectives and waterbody type.

36


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o Micro-scale: sampling locations must be determined by site accessibility and
physical configuration.

For more information, go to guidebook aage 3-43.

USGS Sampling station (photo by A. McGowan, USGS)

2.7 Choose Sample Type

•	Determines the spatial representation of each sample taken at the specific location.

•	Considerations:

o What is the waterbody type?

o Will samples represent the conditions being monitored?
o Are there logistical constraints?

2.7.1	Overview

•	The goal of collecting water samples is to obtain information representative of the
target population for the monitoring effort.

•	Questions to ask include:

o Is monitoring directed only at storm flows?
o Are base flow conditions important to know?
o Do you need to estimate pollutant loads?

o Is monitoring directed at specific conditions that threaten or harm aquatic life?

2.7.2	Basic Types of Samples

•	Four basic types of water quality samples:

o Grab—A discrete sample taken at a specific point and time,
o Composite—A series of grab samples collected at different times and mixed
together.

¦	Time-weighted—A fixed volume of sample collected at prescribed time
intervals and then mixed together.

¦	Flow-weighted—A series of samples, each taken after a specified volume
of flow has passed the monitoring station, that are then mixed together.

37


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o Integrated—Multi-point sampling that accounts for spatial variations in water

quality within a water body,
o Continuous—Truly continuous or very frequent sequential measurements using
electrometric probes.

For more information, go to guidebook page 3-33.

2.7.3 Sample Type as a Function of Monitoring Objective

For more information, go to guidebook page 3-33.

Objective

Monitoring type

Grab

Time-
weighted
composite

Flow-
weighted
composite

Integrated

Continuous

Problem identification &
assessment

X

X

X

X

X

NPS load allocation





X





Point source wasteload
allocation



X

X





Trend analysis

X

X

X

X



Assess watershed project
effectiveness



X

X





Assess BMP effectiveness



X

X





Assess permit compliance

X

X

X





Validate or calibrate models



X

X

X



Conduct research



X

X

X

X

2.7.3.1 Grab Samples

•	Definition—Discrete samples taken at a specific point and time.

o Give a narrow representation of spatial and temporal variability,
o Are obtained manually or through automatic samplers using plastic or glass
bottles/jars.

o Are used for wadeable streams, from boats on lakes, or from bridges during high
flows.

•	Challenges of grab samples include:

o Exact location must be documented.

o Sample content is significantly influenced by the specific method used,
o See Isokinetic vs. Nonisokinetic grab sample methods

For more information, go to guidebook page 3-35.

38


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Collecting grab samples (photo by USEPA)

2.7.3.1.1 Grab Samples: Isokinetic vs. Nonisokinetic

•	Wilde et al, (2014) define samples for which the velocities of the stream and water
entering the sampler intake are the same and different as isokinetic and nonisokinetic,
respectively.

•	Example: Isokinetic vs nonisokinetic samples of stream water.

o Because the suspension of particulate materials depends largely on the stream
velocity, an isokinetic sample might have a different and more accurate
sediment concentration compared to a nonisokinetic sample.

•	Nonisokinetic samplers include the hand-held bottle, the weighted-bottle sampler, the
biological oxygen demand (BOD) sampler, and the so-called "thief samplers" such as
the Kemmerer and Van Dorn samplers that are often used for lake sampling at specific
depths.

2.7.3.2 Composite Samples

•	Definition—A series of grab samples collected at different times and mixed together
(collection is time-weighted or flow-weighted).

o Usually collected with automatic samplers.

o Time-weighted composites are used when flow is not a factor or is constant.

o Flow-weighted samples are better for capturing the influence of peak
concentrations and peak flows.

•	Challenges of composite samples include:

o Collecting flow-weighted samples requires an established stage-discharge

relationship, prediction of flow conditions during sample collection, continuous
flow measurement, and instantaneous and continuous calculation of flow
volume that has passed the sampling station.

o Combining simple grab samples at a single location will not reflect spatial
variability.

o Sample preservation (acidification, refrigeration) is often required.

For more information, go to guidebook »age 3-35.

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2.7.3.3 Integrated Samples

•	Definition—Multi-point sampling that accounts for spatial variations in water quality
within a water body.

•	Choose integrated samples when water quality is known to be spatially variable.

o Horizontal integration for rivers
o Vertical integration for lakes

•	Rivers and streams—Collecting isokinetic, depth-integrated, discharge-weighted
samples is standard procedure.

•	Lakes—Mix grab samples taken from each stratum by obtaining a simultaneous
sample of the entire water column with a hose or by automatic devices that collect
water at different depths over time.

•	Integrated grab samples are a useful sample type for lakes because the temporal
variability of lake conditions is generally not as large as that found in streams.

•	Grab samples at various lake depths can provide additional information not captured
by integrated grab samples,

•	Combining seasonal, integrated and simple grab samples taken at representative
depths is a preferred approach for problem assessment and trend analysis for lakes
and other still water bodies.

•	Isokinetic, depth-integrating methods are designed to produce a discharge-weighted
(velocity-weighted) sample.

•	Using this method, each unit of stream discharge is equally represented in the sample,
either by dividing the stream cross-section into intervals of equal width (EWI) or equal
discharge (EDI) (Wilde 2006).

Lake sampling (photo by USE PA)

• Isokinetic depth-integrated samplers—Accumulate a representative water sample
continuously and isokinetically (water approaching and entering the sampler intake
does not change in velocity) from a vertical section of a stream while transiting the
vertical at a uniform rate,
o These are often used for suspended sediment sampling.

40


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•	Challenges of depth-integrated samplers:

o Some devices can require frequent maintenance,
o Can be impractical in northern climates because of ice.

•	Nonisokinetic samplers—The sample enters the device at a velocity that differs from
ambient.

o Types include hand-held open-mouth bottles, weighted bottles on cables, and
specialized biological oxygen demand and volatile organic compound samplers.

•	Depth-specific samplers— Used to collect discrete samples from lakes, estuaries and
other deep water at a known depth.

o Common types include the Kemmerer and Van Dorn samplers.

For more information, go to guidebook )age 3-36 and 3age 3-71.

A. Kemmerer sampler s. Van Dorn sampler

41


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2.7.3.4 Continuous Samples

•	Definition—Truly continuous or very frequent sequential measurements using
electrometric probes.

o Useful for trend analysis or to assess BMP or watershed project effectiveness

(e.g., tracking exposure of aquatic organisms to harmful levels of DO),
o Can track the duration of values exceeding thresholds (in particular, those with

significant diurnal variability),
o Can measure flow or in situ parameters (e.g., temperature and DO).

•	Challenges of continuous sampling include:

o Requires careful field observation and sensor cleaning/calibration,
o Provides no details about the spatial aspects of water quality conditions,
o Collecting too much data requires conducting data reduction and addressing the
problem of autocorrelation.

For more information, go to guidebook tage 3-37.

Continuous water quality monitor deployed off a bridge in Westerly, Rl (photo by J. Morrison, USGS)

2.7A Stage-Discharge Relationship

•	Continuous discharge measurement in open channels usually requires that the stage-
discharge relationship is known, either by installing a weir or flume or developing a
stream rating.

•	A stage-discharge relationship is an equation determined for a specific site that relates
discharge to stage, based on a linear regression of a series of concurrent
measurements of stage and discharge.

•	As shown here, stage-discharge relationships usually take on a log-log form. With a
valid stream rating, discharge can be determined simply from a stage observation
plugged into the equation or read from a table.

For more information, go to guidebook page 3-20.

42


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Stream stage H (m)

Q = 42.17(H)1-302

2.7.5 Choose Sample Type—Summary

• Have you decided which of the following sample types are most appropriate for your
study?
o Grab
o Composite
o Integrated
o Continuous

2.8 Select Variable

Determine variables that best meet the program objectives with due consideration to
available resources.

Considerations:
o Which variables best support your project goals?

o How many variables should you choose? (Note: It's sometimes better to focus
efforts on monitoring a small set of variables.)

2.8.1 Overview

•	Monitoring variables are often grouped into three main categories:

o Physical (e.g., flow, temperature, suspended sediment)
o Chemical (e.g., dissolved oxygen, total phosphorus, pesticides)
o Biological (e.g., bacteria, benthic macroinvertebrates, fish)

•	Issues to keep in mind:

o Use resources carefully by selecting only those variables that are necessary,
o Pick specific variables that are important to the study instead of a generic list of
traditionally monitored variables.

43


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2.8.2 Select Variables

This section will cover the following factors related to selecting variables:

Factor

Questions to ask

Program objectives

Are the objectives well-defined?

Waterbody designated use

What are the waterbody's designated uses and is it impaired?

Water resource type and
pollutant source

What is the type of water? What is causing the pollution, and can you measure
the water's response to treatment?

Cost of analysis

What analytical methods are available, and are there ways to reduce analytical
costs?

Logistical constraints

How will you manage holding times and constraints?

Covariates

What are the important covariates to measure?

2.8.2.1	Program Objectives

•	In many cases, the program objective will clearly indicate the appropriate variable(s)
to monitor.

o Example: If your objective is to reduce phosphorus loading to a lake, suggested
variables would be phosphorus and flow because measuring both concentration
and flow are required to calculate load.

•	It's more challenging to select monitoring variables when program objectives are less
specific.

o For monitoring aimed at assessing water quality standards compliance, your
variables should focus on what is required to assess violations of water quality
standards.

o For monitoring objectives that involve watershed reconnaissance or
characterization, your choice of variables must consider the nature of the
impairment, type of water resource, and likely pollutant sources.

For more information, go to guidebook page 3-2.

2.8.2.2	Waterbody: Designated Use

•	Variable selection can be driven by a waterbody's designated use. Designated uses are
one of three elements contained in water quality standards. Typical designated uses
include:

o Protection and propagation offish, shellfish, and wildlife

o Recreation

o Public drinking water supply

o Agricultural, industrial, navigational and other purposes

•	States and Tribes designate water bodies for specific uses based on their goals and
expectations for their waters.

44


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•	Water quality criteria are set to protect each designated use by describing the
chemical, physical and biological conditions necessary for safe use of waters by
humans and aquatic life.

•	These criteria should help guide variable selection and other monitoring details (e.g.,
sampling period, frequency) where use attainment or protection is the primary
monitoring concern.

•	Monitoring waterbodies with use impairments can differ substantially from
monitoring to assess use attainment or protection.

o Example: The impairment could be the result of a single pollutant, rather than a
failure to meet all applicable water quality criteria.

•	Monitoring can be focused on the specific variables that are violating criteria instead
of all potential variables.

•	Although the variable list associated with criteria can be narrowed, additional
variables should be considered to address the causes of the violation(s).

For more information, go to guidebook page 3-2.

2.8.2.3	Water Resource Type and Pollutant Source

•	Type of Water Resource—Appropriate variables often differ between surface and
groundwater and between streams and lakes.

•	Pollutant Source—Variables monitored should reflect the NPS pollutants known or
suspected to be present in the watershed.

o Crop agriculture is likely to influence suspended sediment, turbidity, nutrients
and pesticides measured in water.

o Intensive livestock agriculture in a watershed would justify measuring biological
oxygen demand, nutrients and indicator bacteria.

o Urban stormwater sources are likely to influence variables such as discharge,
temperature, turbidity, metals and indicator bacteria.

For more information, go to guidebook page 3-3.

2.8.2.4	Cost of Analysis

•	The choice of suitable variables can be influenced by the cost of analysis if you have
budget constraints.

•	Ways to reduce costs:

o Use an in-house laboratory, such as a university or a state agency.

o Select alternate variables that cost less.

¦	Turbidity instead of suspended sediment.

¦	Specific conductance instead of total dissolved solids.

o Use a less-costly analytical method (if sensitivity is acceptable).

For more information on overall monitoring costs see Chapter 9 of the guidebook.

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2.8.2.5	Logistical Constraints

•	Most water quality variables have specified permissible holding times and holding
conditions (i.e., refrigeration), which determine the length of time a sample can be
stored between collection and analysis without significantly affecting the analytical
results.

•	Questions to ask:

o Is refrigeration necessary?

o Is there adequate power to planned locations of automated samplers or
continuous flow measurements?

o Can the samples be delivered to the lab under the required conditions within the
specified holding time?

For more information, go to guidebook page 3-2.

2.8.2.6	Covariates

•	Covariates are variables that are not directly required by project objectives or
pollutant sources but might be important in understanding or explaining the behavior
of other critical variables.

•	Examples of covariates:

o Precipitation and other weather variables are often collected to explain pollutant
loading and transport.

o Flow or stage measurements can help explain observed patterns of suspended
sediment or particulate phosphorus that are delivered predominantly in surface
runoff during high-flow events.

o Temperature, chlorophyll o and algae are related to nutrient loading in lakes.

For more information, go to guidebook page 3-9.

2.8.3 Response to Treatment

•	When a monitoring program is designed to evaluate water quality response to
implementation of a management measure, you must monitor variables that focus on
the dimensions of water quality expected to change in response to treatment.

o Example: For an agricultural watershed that uses a suite of conservation
practices to address an erosion problem, your monitoring program should
measure flow, peak flow, suspended sediment and turbidity because these
variables are likely to respond to widespread changes from conventional
cropping practices.

For more information, go to guidebook page 3-4.

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2.8.4 Method Comparability

•	Advances in sampling and analytical methods can reduce interference and improve
reliability and accuracy.

•	Difficulties can arise when advances occur during a current project or when trying to
design a new project that uses historical data.

•	Ensuring that samples can be compared is critical.

o One option is to perform a comparability study by implementing both methods

with laboratory splits and comparing the resulting paired data,
o For a project of limited duration, sometimes it's best to continue with an older
method rather than updating to a new method.

For more information, go to guidebook page 3-7.

2.8.5	Set Priorities

•	Because there are many water quality variables to choose from, it's important to take
a deliberate approach to setting priorities when designing a monitoring program.

o Prepare a justification for each candidate variable,
o Consider a ranking system where:

¦	A minimum set of essential variables are identified.

¦	A set of additional, justifiable variables is included if other constraints allow,
o Conduct a systematic evaluation of correlations among candidate variables to

determine:

¦	Are any variables highly correlated?

¦	If so, do they both need to be measured?

For more information, go to guidebook page 3-9.

2.8.6	Select Variables—Summary

•	Have you considered the following when selecting your variables?

o	Program objectives

o	Type of water resource

o	Pollutant source

o	Cost of analysis

o	Logistical constraints

o	Covariates

2.9 Design Stations

•	Determine the best way to design and operate the physical facilities* involved in fixed
monitoring stations.

•	Considerations:

o What are your project objectives?
o Is there a need for fixed monitoring stations?

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2.9.1 Overview

•	Not all monitoring designs require fixed station facilities. When they are required,
several important principles apply:

o Select monitoring sites according to specific criteria based on program
objectives and needs.

o Design the station to collect representative samples from the target population

under foreseeable circumstances,
o Strive for simplicity,
o Include redundancy,
o Provide security.

For more information, go to guidebook page 3-56.

2.9.2	Grab Sampling Stations

•	Monitoring programs based solely on grab sampling might not require stations with
physical facilities; however, the selected monitoring site must be located and
identified so that samples can be repeatedly collected from the same location.

o Make sampling sites easy to find (e.g., road crossings on streams, pipes

delivering flow to or from a stormwater treatment system),
o Record stations on a map or in a standard operating procedure,
o Use GPS coordinates for more challenging locations, such as in a lake,
o For depth location, use a weighted line or an electronic depth sounder.

•	Lake and wetland monitoring typically require grab sampling.

For more information, go to guidebook page 3-57.

2.9.3	Fixed Station Design Aspects

The next slides will cover important aspects of fixed station design for several
common applications. (Note: Although fixed stations can be used to monitor
groundwater, they are not covered in the NPS guidebook.)

Application

Measurement types

Perennial streams and
rivers

Stage/discharge equipment, automated samplers, water quality data
loggers, wingwalls, berms

Edge-of-field

Stage/discharge equipment, automated samplers, water quality data
loggers

Structure/BMPs

Passive first flush sampler, flume inserts for pipes

Meteorological

Meteorological station, rain gauge

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2.9.3.1 Perennial Streams and Rivers Sampling

•	Long-term stations used to continuously record streamflow and collect periodic water
samples require structures and facilities to house monitoring equipment,

•	Continuous flow measurements require a staff gauge and a way to continuously
record stage, using:

o A stilling well with a float bubbler. These are highly reliable and are protected

from turbulence, ice and debris in the stream channel,
o A bubbler, pressure transducer or ultrasonic device. These can be placed directly
in the stream channel, data can be logged electronically, and flow data can be
linked to an autosampler.

Satellite antenna

Stream sampling station (image by L.S. Coplin, USGS)

•	Water samples at continuous monitoring stations are typically collected by
autosamplers, which can:

o Pump samples from the stream through plastic tubing and collect the water in

one or more bottles,
o Collect timed samples of specific volume or storm-event or flow-proportional

samples when linked to a flow recorder or other triggering device,
o Operate unattended for extended periods.

o Be linked together with a data logger for sampling control and data storage,
o Be equipped to communicate through cell phone systems or the Internet in real
time, allowing data to be downloaded and commands for sampling or recording
data to be sent remotely,

•	Challenges with using autosamplers:

o Sampler intake is usually fixed at a single point in the stream; samples collected

might not be representative of vertical or horizontal variability,
o Depth-integrated intake devices can require frequent maintenance and can be
impractical in northern climates where ice is a problem.

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o They require electrical power or deep-cycle automotive or marine batteries,

which need servicing and recharging,
o Operation in winter weather might require robust shelter and heating tape or
propane heaters.

o Operation in hot climates might require special cooling/ ventilation.

For more information, go to guidebook >age 3-58 or oage 3-77.

2.9.3.2 Edge-of-F/e/dSampling Stations

•	At edge-of-field, flow is intermittent, and channels might not be defined.

•	Challenges include:

o The need to measure flow (when it occurs),
o The need to collect representative water samples and other data,
o The need for power to run equipment,
o Extreme weather events.

•	Typical edge-of-field stations include:

o Enclosures to house equipment designed to measure stage, collect samples and

provide telecommunication,
o Stage and discharge equipment,
o Sampling equipment,
o Data logging and control instruments
o Communications
o Power
o Camera

•	Stations will be dormant for extended periods but need to be ready for activation.
Regular maintenance visits are required.

For more information, go to guidebook >age 3-60.

Edge-of-field monitoring station, Wisconsin Discovery and Pioneer Farms (Stuntebeck et al. 2008)

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Edge-of-field monitoring station, Wisconsin Discovery and Pioneer Farms (Stuntebeck et at. 2008)

Edge-of-fieid monitoring station, Vermont (Meals et al. 2011)

Edge-of-field monitoring stations, VT (photo by Meals et al. 2011)

2.9.3.3 Structures/BMPs Sampling Stations

•	Many individual BMP monitoring efforts have similar requirements for flow
measurement, water sampling, data logging, communications and security as other
station types, but are often constrained by physical characteristics.

•	Examples:

o Monitoring inflow and outflow from a constructed wetland is generally

comparable to monitoring flow in an intermittent stream,
o Runoff from a parking lot entering an infiltration BMP may be difficult to

quantify and sample; outflow from the BMP may be carried in an underground
pipe.

•	Some specialized equipment for such monitoring has been developed, including
passive runoff samplers and flume inserts for pipes with integrated stage sensors.

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Manhole

Flow measurement and water quality sampling in stormwater pipes (USEPA 2016)

Street runoff sampler (image from Waschbusch et al. 1999)

•	In urban runoff monitoring, the first-flush phenomenon requires special consideration
because pollutant loads during the first part of an event may be much larger than
those in the later flows.

•	Examples of first flush runoff samplers are shown below.

•	Monitoring the input/output of a BMP requires two monitoring stations that are
coordinated but not simultaneous.

•	If sampling is conducted simultaneously at the entrance and exit of a BMP, the
outflow sample may represent "old" water pushed out of the BMP by "new" inflow,
rather than new inflow after treatment by the BMP.

•	Time of travel or residence time in the BMP must be considered in setting up
monitoring stations. Establishing links between the upstream and downstream
stations allow for better coordination between them. An example of time of travel is
below.

For more information, go to guidebook lages 3-60 to 3-61.

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A. Nalgene® first-flush sampler.
Installed below grate (at right).

C. GKY first-flush sampler.

Images from USEPA 2016

2.9.3.3.1 Time of Travel Example

•	Stuntebeck et a!. (2008) modified the basic above/beiow design in a Wisconsin
barnyard runoff study by setting the samplers to be activated by precipitation and
programming them to collect time-integrated samples for an initial period,

o This modification allowed for sampling of barnyard runoff in the receiving stream
before stream water level increases could be sensed, thereby effectively
isolating the barnyard runoff from nonpoint pollution sources upstream.

o This approach allowed sampling during small storms in which local inputs from
the barnyard were apparent, but little storm runoff from the upstream areas of
the watershed were observed.

o A second modification took advantage of the close proximity of the two stations
to create a direct electronic connection between the stations for collection of
concurrent samples.

2.9.3.4 Meteorological Sampling Stations

•	Meteorological data, particularly precipitation data, are nearly always relevant to NPS
monitoring projects.

•	Most important criterion for precipitation measurement = location.

o For BMP or field monitoring efforts, a single meteorological station may be
sufficient.

o For larger watershed monitoring, multiple stations are usually necessary to
account for variations of weather with elevation and other geographic factors.

o Multiple precipitation stations are used when data are needed for model
application.

o Stations must be unobstructed to obtain accurate measurements.

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• Instrumentation:

o Electronic instruments record directly into dataloggers.

o Tipping bucket rain gauges measure both total accumulated rainfall and rainfall
rate. They can be connected to other monitoring instruments to log data and/or
trigger sample collection.

For more information, go to guidebook >age 3-67.

Meteorological monitoring station (Meals et al. 2011)

2.9.4 Design Stations—Summary

•	Are fixed stations necessary in your program for the following types of continuous
monitoring?

o	Perennial streams and rivers

o	Edge-of-field

o	BMPs/structures

o	Meteorological measurements

2.10 Define Collection & Analysis Methods

•	Collection and analysis of samples requires training, appropriate equipment, careful
adherence to standard procedures and detailed record keeping.

•	Considerations:

o Can you align your proposed methods with those used in the past?
o Are the methods you want to use approved by a reliable source?

2.10.1 Overview

•	Documentation and records

o Use field sheets, SOPs and logbooks.

•	Preparation for sampling

o Cleaning, calibrating and testing equipment.

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•	Cleaning

o Use clean sample containers to avoid contamination,

•	Safety

o Don't work alone,
o Pay attention to weather,
o Use safety devices when flow is high.

Collecting samples from a bridge (photo by NRCS)

2.10.2 Data Collection and Analysis Options

This section covers different types of field measurements, methods of sample collection,
information on sample handling and transport, and laboratory considerations.

Field
measurements

Sample collection

Sample processing,
transportation and analysis

Laboratory

Single point

Grab

Processing

Type of lab

Multiple points

Passive

Storage, preservation and transport

Methods used

In situ or onsite

Autosampling

Chain-of-custody

Certifications

Groundwater

Benthic macroinvertebrates

Performance audits





Aquatic habitat







Fish







Aquatic plants







Pathogens







Specialized





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2.10.2.1 Field Measurements

•	Variables such as water temperature and DO concentration must be measured directly
in the waterbody; properties such as pH, specific conductance and turbidity can be
measured either in situ or immediately on the site using a sample taken from the
source.

•	In flowing water, a single sampling point in a well-mixed area is generally used to
represent an entire cross-section.

•	In lakes or other still water, field measurements might be made at multiple locations
and depths.

•	Groundwater generally requires purging the monitoring well of standing water and
then taking field measurements.

For more information, go to guidebook >age 3-70.

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2.10.2.2 Sample Collection

2.10.2.2.1	Sample Collection: Grab Sampling Collection Methods

•	Grab sampling can be done manually by dipping a sample bottle by hand under the
water at a certain depth. Proper procedures must be followed.

•	As already described in the Choose Sample Type section, a variety of devices are
available to collect grab samples from waterbodies for different purposes:

o Isokinetic depth-integrated samplers
o Nonisokinetic samplers
o Depth-specific samplers

For more information, go to guidebook >age 3-71.

2.10.2.2.2	Sample Collection: Passive Sampling Collection Methods

•	Passive samplers collect unattended grab samples without relying on external power
or electronic activation. The exact time and circumstance of sampling is unknown
unless other data are taken at the same time.

•	Examples of passive samplers include:

o	Runoff samplers

o	Single-stage samplers

o	Tipping-bucket samplers

o	Coshocton wheel samplers

o	Lysimeters

For more information, go to guidebook page 3-73.

Passive runoff sampler/flow splitter, University of Georgia, Tifton, GA (photo by D. Meals, USEPA)

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2.10.2.2.3 Sample Collection: Autosampling Collection Methods

•	Autosamplers generally consist of:

o An intake line submerged in the waterbody or the flow through a pipe or flume
o A peristaltic or submersible pump that pumps water to the sampler
o One or more bottles to contain collected samples
o Electronic controls to initiate sample collection and record data

•	Some autosamplers might be refrigerated to preserve samples for extended periods.

•	Some autosamplers might be designed specifically to fit into storm drains and catch
basins.

•	Most autosamplers operate with either DC or AC power.

•	Autosamplers can be set to take time-based samples either continuously (e.g., collect
a sample every 8 hours) or as initiated by an external trigger (e.g., detection of rainfall,
rising stream stage).

•	When connected to a flow meter, autosamplers can take flow-proportional samples,

•	Autosamplers can collect discrete samples in individual bottles or a composite sample
in one large container.

A portable autosampler (photo by Teledyne Isco, 2013)

• Disadvantages with autosamplers include the following:

o Intakes are generally fixed in one position in a waterbody and therefore might
not fully represent variability, especially where strong vertical or horizontal
gradients exist.

o The size of the intake line and the velocity achieved by the autosampler pump, as
well as the position in the streamflow, might prevent collection of a representative
sample, especially of suspended sediment and particulate-bound pollutants,
o Monitoring for some pollutants like volatile organics or pathogens could be
challenging because of special limitations for materials that contact the sample
and requirements for sterilization between sample-intake events,
o Because samples are taken at intervals, regardless of whether an autosampler
collects on a time- or flow-based program, the possibility always exists that a
transient pulse of a pollutant (e.g., from a spill or first-flush) may pass by
unsampled. (This, of course, is also a risk in manual sampling.)

For more information, go to guidebook page 3-77.

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2.10.2.2.4 Sample Collection: Benthic Macroinvertebrate Sampling

•	Sampling of benthic macroinvertebrates from stream bottoms and lake beds must
consider:

o How to physically collect samples.

o The diversity of stream habitats that influence the numbers and types of
organisms,

•	The habitats sampled should be based on monitoring objectives and regional stream
or lake characteristics,

•	in streams, two distinct habitats are generally sampled: riffles and pools.

•	In lakes, substrates and habitats vary between near-shore areas and deeper lake
regions; thus, organisms will differ, and different sampling approaches will be needed.

Using a D-frame net to sample a gravel-bottom stream for benthic macroinvertebrates (USEPA 2016)

•	Active sampling:

o In rivers and streams, active collection is often accomplished by disturbing the
streambed and capturing the dislodged organisms in a net as the current carries
them downstream,

¦	Kick-seines, D-frame nets and Surber square-foot samplers are common
devices used.

¦	It's important to quantify both the area of the streambed disturbed and the
time/effort of sampling so that results can be quantified (e.g.,
organisms/m2), repeated and compared overtime.

o In lakes, active sampling in shallow areas can be done by similar methods.

¦	Grab samplers, such as the petite ponar or larger dredges, are used for
collecting sediment samples from hard bottoms (e.g., sand and gravel).

•	Passive sampling:

o Uses artificial substrates like the Hester-Dendy plate sampler or rock baskets
that are anchored in the waterbody. After organisms colonize them, they are
retrieved and counted.

For more information, go to guidebook 3age 3-78.

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2.10.2.2.5 Sample Collection: Aquatic Habitat Assessment Methods

•	Assessing aquatic habitat is important for interpreting data collected from monitoring
of benthic invertebrates and fish. Habitat characteristics can be response variables for
land treatment or stream restoration efforts.

•	Habitat quality is typically measured in three dimensions:

o Habitat structure: Includes physical characteristics of stream environment, such
as channel morphology, gradient, instream cover, substrate types, riparian
condition and bank stability,
o Flow regime: Defined by velocity and volume of water moving through a stream,

both the average and during extreme events (wet or dry),
o Energy source: Energy enters stream systems through nutrients from runoff or
groundwater (as leaves/other debris falling into streams) or from photosynthesis
by aquatic plants and algae.

For more information, go to guidebook )age 3-78.

2.10.2.2.6 Sample Collection: Fish Sampling Collection Methods

•	As with benthic macroinvertebrates, distinct fish assemblages are found in different
habitat types.

•	Water temperature, flow, dissolved oxygen, cover and shade, and substrate type are
important habitat characteristics.

•	Major habitat types like riffles, pools and runs should be sampled.

•	Habitats and the size of sampling areas should be consistent between sampling events
to allow for long-term comparisons.

•	Fish are most commonly sampled by electrofishing, but seines, gill nets, traps or
underwater observations are also used.

For more information, go to guidebook iage 3-80.

Backpack electrofishing (photo by USEPA)

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2.10.2.2.7 Sample Collection: Aquatic Plant Sampling Collection Methods

•	Aquatic plants sampled for water quality monitoring include:

o Algae: small free-floating plants

o Periphyton: the community of algae, microbes and detritus attached to

submerged surfaces
o Macrophytes: large plants rooted in aquatic sediments

•	Many of these plants are good indicators of nutrient enrichment and ecosystem
condition.

•	Algae are sampled using a plankton net towed through the water column; organisms
are identified and counted under a microscope.

•	As a surrogate for algal biomass, chlorophyll a can be measured.

•	Periphyton biomass is usually measured in streams, either by scraping known areas of
rock surfaces or by using artificial substrates.

•	Nearshore aquatic macrophytes might be surveyed to assess species composition,
quantified in small plots, or mapped by remote sensing to document areal extent of
growth.

For more information, go to guidebook page 3-82.

Aquatic plants in a Washington wetland (photo by NRCS)

Trawling with a plankton net (photo by NOAA 2005)

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2.10.2.2.8	Sample Collection: Bacteria/Pathogen Sampling Collection Method

•	Indicator bacteria, pathogens, or other microorganisms are usually collected by grab
sampling.

o Example sample volumes:

¦	E. coli bacteria analysis requires small volumes (e.g., 100 mL).

¦	Giardia and Cryptosporidium might require up to 20 L.

•	Requires sterile sample containers (e.g., pre-sterilized, single-use bags/bottles, or
autoclaved polyethylene containers).

•	Sample collection should be done by clean technique, with samples allowed to contact
only sterile surfaces; field personnel should wear gloves.

•	Samples typically require more rapid delivery to the laboratory than samples from
physical and chemical analyses.

For more information, go to guidebook page 3-82.

2.10.2.2.9	Sample Collection: Specialized Sampling Collection Methods

•	Specialized sampling techniques are sometimes needed for unusual or emerging
pollutants.

o Microbial source tracking requires water sampling and can involve collecting

fecal material from human and animal sources in the watershed,
o Urban stormwater monitoring can involve tests for optical brighteners as

indicators of wastewater or septic effluent contamination—this requires cotton
pads to be deployed in streams for several days, collected, and then tested for
fluorescence with an ultraviolet light source,
o Sentinel chambers, dialysis membrane diffusion samplers, polar organic chemical
integrative samplers (POCIS), and other passive sampling devices have been used
to passively sample low-concentration pollutants like VOCs, estrogen analogs,
endocrine disruptors, and other emerging pollutants in a variety of settings.

For more information, go to guidebook page 3-83.

2.10.2.3 From Field to Laboratory: Sample Processing, Transportation and Analysis

•	There are several important steps to consider between sample collection and analysis,
including:

o	Sample processing

o	Sample preservation and transport

o	Sample custody tracking

o	Performance audits

For more information, go to guidebook page 3-84.

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2.10.2.3.1 Sample Processing

•	Sample processing refers to the measures taken to prepare and preserve a water
sample at or after collection, but before it's delivered to the laboratory for analysis.

•	Goals are to prepare samples for analysis, prevent contamination and cross-
contamination, and preserve sample integrity until analysis,

o Samples requiring filtration must be filtered during or immediately after collection,
o Surface water samples might be composited or subsampled in the field using an

appropriate device, such as a churn or cone splitter,
o Groundwater samples are not composited but are pumped either directly
through a splitter or through a filtration assembly into sample bottles (unless a
bailer or other downhole sampler is used to collect the sample).

Cone filter (photo by FISP 2014)

2.10.2.3.2	Sample Storage, Preservation and Transport

•	Water samples to be analyzed for most water quality variables have specified
permissible holding times and holding conditions

o For more details, see Table 3-12 in the guidebook.

•	Storage and preservation for most analytes involve:

o	Cooling

o	Using chemical preservatives

o	Getting sample to the lab quickly

o	Using proper packaging when shipping

o	Using proper labeling and documentation

2.10.2.3.3	Sample Chain of Custody

•	The location and status of collected samples must be tracked at all points to:

o Prevent loss of samples and data.

o Document the conditions under which the samples were held,
o Preserve sample and data security and integrity.

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•	Sample custody starts with a consistent numbering and labeling system that uniquely
identifies each sample's source, monitoring program, date and time of collection,
responsible person(s) and desired analysis.

•	Custody is tracked using forms and other records that are signed and dated by each
individual in the chain.

2.10.2.3.4 Performance Audits

•	Regular field operations performance audits should be part of the overall quality
assurance/quality control process. These audits include:

o Sample container and equipment blanks: Distilled/deionized water is processed

through sampling equipment and sample containers to rule out contamination,
o Trip blanks: Distilled/deionized water is transported from the laboratory through
the field sampling process to document any potential contamination acquired
during travel and transport,
o Field duplicates: Two grab samples are collected in quick succession to assess

repeatability of sampling,
o Field splits: A collected sample is split into two subsamples to assess analytical
performance by the laboratory or to make comparisons between labs.

2.10.2.4 Laboratory Considerations

•	Type of lab: The accuracy and precision generally required in NPS monitoring
programs require formal laboratory analysis. Laboratories are typically operated by
state agencies, universities or private companies.

•	Methods used: Analyses should be conducted using accepted laboratory methods.

•	Certification: Use a laboratory certified either by a state program or the USEPA
Drinking Water Program.

•	In addition to the above considerations, also look for a laboratory that:

o Participates in regional comparative proficiency testing programs,
o Provides documentation of methods and QA/QC protocols used,
o Provides assurance that samples will be handled and processed expeditiously.

For more information, go to guidebook page 3-90.

2.10.3 Define Collection and Analysis Methods—Summary

•	Have you determined which of the following collection methods you will need?

o	Field measurements

o	Grab sampling

o	Passive sampling

o	Autosampling

o	Benthic macroinvertebrate sampling

o	Aquatic plant sampling

o	Bacteria/pathogen sampling

o	Habitat sampling

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o Specialized sampling

•	Have you planned for all steps from sample processing to laboratory analysis?

2.11 Define Land Use Monitoring

•	Determine what land use activities are generating NPS pollution and how to
effectively monitor them.

•	Considerations:

o How will you track both land use and land treatment?
o How will you link land treatment to water quality response?

2.11.1	Overview

•	NPS pollution is generated by activities on the land that vary in location, intensity and
duration.

o Land use refers not only to the general category of land use or cover (e.g.,
residential, row crop) but also to land management or source activities (e.g.,
street sweeping, agrichemical applications, tillage),
o Land treatment refers not just to the existence of a specific treatment or BMP
(e.g., sediment basin, reduced tillage) but also to the management of the BMP
(e.g., sediment basin clean-out, tillage dates, nutrient application rate, timing
and method).

For more information, go to guidebook page 3-91.

2.11.2	Link Land Treatment to Water Quality Response

•	Linking land treatment to water quality response requires both land use/treatment
and water quality monitoring.

•	Specific needs can differ by monitoring type.

•	Understanding pollutant loading patterns requires information about both the spatial
and temporal variability of source activities.

•	It's necessary to track land use/treatment when planning to attribute water quality
trends to activities on the land.

•	Because monitoring for trend analysis can continue for decades, consider costs when
deciding about the scope, level of detail, and frequency of monitoring that will be
done.

For more information, go to guidebook page 3-91.

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2.11.3 Define Land Use Monitoring

The following sections will cover these different aspects of land use monitoring.

Topic

Example

Activities to monitor

Consider land use/land cover and BMPs—and the associated management of each.

Methods of data
collection

Options include direct observation, logbooks, interviews, agency reporting and remote
sensing.

Temporal and
spatial scale

What land area contributes to the water being sampled?

Should you match the temporal scale to that of the water quality monitoring?

Variables

Match the land use/treatment variables to the water quality variables.

Frequency

Choose frequency based on whether your land use/treatment data is static or dynamic.

For more information, go to guidebook page 3-91.

2.11.4	Important Things to Document

•	For individual BMP effectiveness monitoring, it's important to document:

o The design specifications of the practice evaluated.

o The degree to which the practice was implemented, maintained and operated

according to specifications,
o Management activities conducted under the scope of the practice,
o Any situations where the BMP operated under conditions outside of the design
range.

For more information, go to guidebook page 3-91.

2.11.5	Basic Methods

•	The basic methods used to monitor land use and land treatment are:

o	Direct observation

o	Logbooks

o	Interviews

o	Agency reporting

o	Remote sensing

For more information, go to guidebook page 3-92.

2.11.6	Direct Observations

•	Personal observations might be the best way to track land use/treatment for plot and
field studies.

•	Common types of observations include:

o Tracking forms
o Windshield surveys
o Photography

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• Disadvantages of direct observation methods:

o Potential for bias due to lack of understanding of activities
o An established schedule misses important events
o The inability to assess information about rate or quantity

For more information, go to guidebook page 3-92.

•	Logbooks can be given to landowners and managers to record activities relevant to
the monitoring study.

•	Advantage of this method: the same individual who is responsible for the activity does
the reporting.

•	Disadvantage: it's difficult to guarantee compliance or consistent reporting between
individuals.

For more information, go to guidebook page 3-93.

2.11.8 Interviews

•	When conducted in person, interviews offer the opportunity to gather additional
information that is important to the study.

•	Disadvantages of interviews include:

o Potential for less-than-complete reporting of information by the person
interviewed.

o Potentially inadequate or uneven interview skills by those conducting the
interviews.

o A combination of the logbook and interview approach works well in small
watersheds with a relatively small number of participants.

For more information, go to guidebook page 3-93.

Photo by Minnesota Department of Natural Resources

2.11.7 Logbooks

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2.11.9 Agency Reporting

Land use data are available through many different agencies, including:

Data source

(Summaries provided in following
section)

Link to more information
(Click to visit Web page)

Soil and Water Resources Conservation Act
(RCA) Report-Interactive Data Viewer

https://www. nrcs.usda.gov/wDs/oortal/nrcs/rca/national/tech

nical/nra/rca/ida/

USDA's National Resources Inventory (NRI)

https://www.nrcs. usda.gov/wDs/Dortal/nrcs/main/national/tec

hnical/nra/nri/

Census of Agriculture

httos://www. nass.usda.gov/Publications/AgCensus/2012/

NOAA's Coastal Change Analysis Program's
(C-CAP)

httos://coast. noaa.gov/digitalcoast/data/ccaoregional. html



National Land Cover Database (NLCD)

httos://www. mrlc.gov/

U.S. Census Bureau's TIGER (Topologically
Integrated Geographic Encoding and
Referencing) Program

httDs://www. census.gov/Drograms-

surveys/geograDhv/guidance/tiger-data-Drod ucts-guide.html



Water Quality Portal

httDs://www.waterqualitydata.us/

For more information, go to guidebook page 3-94.

2.11.9.1	RCA Report-Interactive Data Viewer

•	USDA maintains data on conservation practices implemented with USDA cost-share
funds or technical assistance. State-level information can be obtained through the Soil
and Water Resources Conservation Act (RCA) Report-Interactive Data Viewer.

•	The RCA authorizes USDA to report on the condition of natural resources, and to
analyze conservation programs and opportunities. The Interactive Data Viewer
provides data from a variety of sources, including data on the status and trends of
natural resources, conservation efforts (funding and conservation practices applied),
and the agricultural sector.

2.11.9.2	USDA's National Resources inventory

•	USDA's National Resources Inventory (NRI) provides survey-based inventories of land
use information.

•	The NRI program collects and produces scientifically credible information on the
status, condition, and trends of land, soil, water, and related resources on the Nation's
non-federal lands in support of efforts to protect, restore, and enhance the lands and
waters of the United States.

•	NRI survey results are based upon a particular set of definitions, protocols, and
instructions. These have been developed to support NRCS programs and USDA
analytical needs, so they differ in some cases from those used by other agencies.

These differences need to be considered when analyzing/interpreting the data.

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2.11.9.3	Census of Agriculture

•	USDA's National Agricultural Statistics Service (NASS) conducts the Census of
Agriculture once every 5 years. It's a comprehensive summary of agricultural activity
for the U.S. and for each state. It includes the number of farms by size and type,
inventory and values for crops and livestock, operator characteristics, and other
information.

•	NASS publishes only aggregated data. NASS is bound by law (Title 7, U.S. Code, and
CIPSEA, Public Law 107-347)—and pledges to every data provider—to use the
information for statistical purposes only.

2.11.9.4	NOAA's C-CAP

•	NOAA's Coastal Change Analysis Program (C-CAP) has a nationally standardized
database of land cover and land change information for U.S. coastal regions, derived
from the analysis of multiple dates of remotely sensed imagery.

•	Two file types are available: individual dates and change files.

•	C-CAP data form the coastal expression of the National Land Cover Database (NLCD)
and the A-16 land cover theme of the National Spatial Data Infrastructure. The data
are updated every 5 years.

2.11.9.5	National Land Cover Database

•	The National Land Cover Database (NLCD) and USGS's Land Use and Land Cover data
provide historical GIS datasets.

•	The Multi-Resolution Land Characteristics (MRLC) Consortium is a group of federal
agencies who coordinate and generate consistent and relevant land cover information
at the national scale for a variety of environmental, land management and modeling
applications. Maps of the lower 48 states, Hawaii, Alaska and Puerto Rico have been
compiled into a comprehensive land cover product from decadal Landsat satellite
imagery and other supplementary datasets.

2.11.9.10 U.S. Census Bureau's TIGER Program

•	The U.S. Census Bureau (USCB) through the TIGER (Topological^ Integrated
Geographic Encoding and Referencing) program provides GIS data for mapping human
population.

•	It includes land features (roads, rivers and lakes), counties, census tracts and census
blocks. Some of the geographic areas represented in TIGER are political areas, while
others are statistical areas.

•	The TIGER program was developed to support USCB's mapping needs for the
Decennial Census and other programs. Every 1-3 years, USCB creates an extract from
this database and releases a TIGER update. These extracts are known as TIGER/Line
files.

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2.11.9.11 Water Quality Portal

•	The Water Quality Portal (WQP) is a cooperative service sponsored by the U.S.
Geological Survey (USGS), USEPA, and the National Water Quality Monitoring Council
(NWQMC). It serves data collected by over 400 state, federal, tribal and local agencies.

•	The WQP combines physical, chemical and biological water quality data from multiple
data sources at one location and provides the data in one format. It provides a single,
user-friendly web interface to access more than 250 million water quality data records
collected by over 400 federal, state and tribal agencies and other water partners.

2.11.10	Remote Sensing

•	Remote sensing can be useful for tracking practices and land management that are
monitored visually.

•	Many remote sensing datasets are available:

o Data products at the USGS's National Map Viewer and Download Platform or

Earth Resources Observation and Science (EROS) Data Center,
o Landsat data, elevation, greenness, "Nighttime Lights," and coastal and Great

Lakes Shorelines (USEPA 2008).
o Low-altitude aerial photography to assess compliance with crop insurance

programs are done annually by the USDA Farm Service Agency,
o Commercial web-based resources such as Bing Maps and Google Earth can be
useful tools for land use monitoring.

For more information, go to guidebook page 3-95.

2.11.11	Temporal and Spatial Scale

•	Land use/treatment monitoring should address the entire area contributing to flow at
the water quality sampling point. Some parts of a larger area might be emphasized
more than others.

o Example: Land nearest to the sampling point can have a major effect on the
measured water quality, so these areas must be monitored carefully. Spatial
coverage of land use monitoring might range from a single field (or portion of a
field) up to an entire river basin.

•	There is often the mistaken assumption that the temporal scale of land use/treatment
monitoring should match that of the water quality monitoring when the data are to be
combined for analyses. Also consider the inherent variability of what is being measured.

o Example: Road salt is applied under icing conditions, while wash-off tends to
occur during periods of thawing or rainfall. Matching weekly water quality and
land use/treatment in this case could result in associating high salinity levels with
periods of no road salt application.

•	The following multi-level monitoring approach can address certain issues with
matching the temporal scales of land use/treatment monitoring to that of water
quality monitoring:

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o Characterization: An initial snapshot of land use/land cover, focusing on static

parameters (e.g., water bodies, highways, impervious cover),
o Annual: A survey for annually varying features such as crop type,
o Weekly: Weekly observations to identify specific dates/times of critical activities

(e.g., manure or herbicide applications, tillage, construction),
o Quantitative: Data collection on rates and quantities (e.g., nutrient or herbicide
application rates, number of animals on pasture).

•	The guiding principle of timing is to collect land use/treatment data at a fine enough
time resolution to be able to explain water quality results as they occur.

For more information, go to guidebook page 3-97.

2.11.12	Monitoring Variables

•	The appropriate set of land use/treatment variables for any monitoring plan will
depend on the monitoring objectives, monitoring design, and characteristics of the
watershed or site to be monitored.

•	The set of variables needed for problem assessment is usually broad, whereas the set
of variables for BMP effectiveness monitoring is tailored to the BMP and the
conditions under which it's being evaluated.

•	Refer to the guidebook for:

o Information on the appropriate selection of land use/treatment variables
(Table 2-2).

o Examples of pairing water quality and land use/treatment variables (Table 3-13)
shows.

For more information, go to guidebook page 3-98 and page 2-4.

2.11.13	Sampling Frequency

•	The frequency for sampling dynamic data will vary depending on the type and
magnitude of the variable's impact on measured water quality.

o For BMP effectiveness studies at the plot or field scale, observations should be

made each time the site is visited,
o Although construction activities might occur daily at any given construction site,
note that certain phases of construction might warrant closer attention.

•	The availability of records should be considered when determining sampling
frequency.

o Many nutrient management plans require producers to keep field-by-field
records of manure and chemical nutrient applications; therefore, sampling can
theoretically be done on an annual basis assuming that the records are clear and
accurate.

For more information, go to guidebook page 3-98.

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2.11.14	Challenges

•	Challenges associated with tracking land use/treatment include:

o Gaining access to locations for direct observation or communication with

landowners or managers,
o Obtaining cooperation on field logs, especially when confidential business

information is involved,
o Checking all source activities of potential interest in a mixed-use watershed can

be logisticaIly difficult, labor intensive and complicated,
o Assuring confidentiality of data to landowners,
o Addressing data gaps when using large-scale agency data.

For more information, go to guidebook page 3-99.

2.11.15	Define Land Use Monitoring—Summary

•	Have you done the following?

o	Determined which land use activities you will monitor,

o	Selected methods for collecting data on each activity,

o	Considered spatial and temporal scale,

o	Selected variables,

o	Selected sampling frequency.

For more information, go to guidebook page 3-99.

2.12 Design Data Management

•	Developing, executing and supervising plans, policies, programs and practices that
control, protect, deliver and enhance the value of data and information assets.
(Mosley et al. 2009)

•	Considerations:

o How will you acquire, store and backup your data?
o Are you using any publicly available data?
o Have you developed a quality assurance project plan (QAPP)?

2.12.1 Overview

•	Data management must be part of initial project planning. It includes:

o	The path the data follows, from generation to final use or storage,

o	Standard record-keeping procedures,

o	Document control system.

o	Approach used for data storage and retrieval on electronic media,

o	Control mechanism for detecting and correcting errors and preventing loss of

data during data reduction, data reporting and data entry,

o	Examples of forms or checklists.

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o Descriptions of data-handling equipment and procedures for processing,

compiling and analyzing data,
o Performance requirements for computer hardware and software.
• Describe the aspects of data management in a QAPP.

For more information, go to guidebook page 3-105.

2.12.2 Design Data Management

The following aspects of data management are presented in the following sections.

Data management topic

Considerations

QA/QC

Develop a QAPP at the beginning of the project and implement and
maintain it throughout the project.

Data acquisition

Consider different issues with manual vs. electronic data entry and
measured data versus data acquired from other sources (e.g., databases,
literature, other programs or agencies).

Data storage

Store manual and electronic data safely. Back up all data.

For more information, go to guidebook page 3-105.

2.12.2.1 Quality Assurance/Quality Control

•	A QAPP details the technical activities and quality assurance/quality control (QA/QC)
procedures that should be implemented to ensure data meet specified standards. A
QAPP should identify:

o Who will be involved in the project and their responsibilities and the nature of

the study or monitoring program,
o The questions to be addressed or decisions to be made based on the data
collected.

o Where, how and when samples will be taken and analyzed,
o The requirements to ensure data quality.

o The specific activities and procedures to be performed to obtain the requisite

level of quality (including QC checks and oversight),
o How data will be managed, analyzed and checked to ensure that they meet the

project goals,
o How the data will be reported.

•	The QAPP should be implemented and maintained throughout a project.

For more information, go to guidebook page 8-1.

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2.12.2.2 Data Acquisition

•	The data generated must be collected (data acquisition) and transferred to the data
management system for storage and analysis.

•	Transcribing field-logged data into a database is a potential source of typographic
errors, switched digits and other errors in data entry.

•	All data must be error-checked after being entered into electronic forms but before
analyses and reporting occurs.

•	Newer methods of data acquisition include the use of data loggers, laptops, tablets
and smartphones.

•	Advantages of Data Acquisition;

o Manual data entry and the associated transcription errors are avoided.

o Remote access allows direct transfer of field data from a data logger to the main
data storage site.

•	Disadvantages of Data Acquisition:

o Storage capacity is limited.

o Once storage capacity is full, any new data might not be recorded, or older data
might be overwritten and thus lost.

•	Other sources of data include computer databases, programs, literature and historical
databases.

o Determine the sufficiency of these data for project purposes. You might need to
ground-truth or fill gaps in the data.

•	Data provided by others might have been collected at different locations, by different
methods or to serve different objectives.

o Carefully review the data and methods used for its collection.

o In the QAPP, include acceptance criteria for the use of such data, as well as any
limitations on data use.

For more information, go to guidebook page 3-105.

Inputting benthic macroinvertebrate sampling data into field sheets (photo by NRCS)

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2.12.2.3 Data Storage

•	All field and laboratory notebooks must be fully documented and stored safely.
Consider creating scanned images.

•	Use spreadsheets for simple projects.

•	Use a relational database for complex projects involving many sites or variables.

•	Back up all computerized data and project files.

For more information, go to guidebook page 3-106.

2.12.3 Design Data Management—Summary

•	Have you done the following?

o	Developed a QAPP.

o	Included data management in the project planning phase,

o	Determined how you will acquire data,

o	Determined how you will store data.

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Photos (Public domain sources): NOAA (National Oceanic and Atmospheric Administration
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