U.S. Department of the Interior

U.S. Geological Survey

Open-File Report 2013–1068

Version 1.1, December 2016

Prepared in cooperation with the City of Boise

Monitoring Plan for Mercury in Fish Tissue and 

Water from the Boise River, Snake River, and 

Brownlee Reservoir, Idaho and Oregon

Monitoring Plan for Mercury in Fish Tissue and Water from 

the Boise River, Snake River, and Brownlee Reservoir, 

Idaho and Oregon 

By Christopher A. Mebane and Dorene E. MacCoy 

Prepared in cooperation with the City of Boise

Open-File Report 2013–1068

Version 1.1, December 2016

U.S. Department of the Interior

U.S. Geological Survey
U.S. Department of the Interior

SALLY JEWELL, Secretary

U.S. Geological Survey

Suzette M. Kimball, Acting Director

U.S. Geological Survey, Reston, Virginia: 2013

First release: 2013, online

Revised: December 2016 (ver. 1.1), online

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Suggested citation:

Mebane, C.A., and MacCoy, D.E., 2013, Monitoring plan for mercury in fish tissue and water from the Boise River, 

Snake River, and Brownlee Reservoir, Idaho and Oregon (ver. 1.1, December 2016): U.S. Geological Survey OpenFile Report 2013–1068, 26 p., http://pubs.usgs.gov/of/2013/1068/.

Any use of trade, product, or firm names is for descriptive purposes only and does not imply 

endorsement by the U.S. Government.

Although this report is in the public domain, permission must be secured from the individual 

copyright owners to reproduce any copyrighted material contained within this report.
iii

Contents

Abstract ...................................................................................................................................................................... 1

Background and Objectives........................................................................................................................................ 1

Project Description...................................................................................................................................................... 3

Monitoring Locations and Frequency ...................................................................................................................... 4

Target Species........................................................................................................................................................ 4

Data-Quality Objectives .......................................................................................................................................... 7

Field Sampling and Sample Processing ..................................................................................................................... 8

Safety and Crew Training........................................................................................................................................ 8

Permits and Coordination...................................................................................................................................... 10

Standard Procedures for Sample Collection and Processing................................................................................ 10

Laboratory Methods.................................................................................................................................................. 12

Mercury ................................................................................................................................................................. 12

Biological Total Mercury in Fish Tissue ............................................................................................................. 12

Total Mercury in Water ...................................................................................................................................... 13

Selenium in Fish Tissue........................................................................................................................................ 13

Quality Assurance and Quality Control ..................................................................................................................... 13

Reporting .................................................................................................................................................................. 14

References Cited...................................................................................................................................................... 15

Appendix A. Excerpt of U.S. Environmental Protection Agency Permit No.: ID-002398-1 Requirements for 

Methylmercury Fish Tissue Monitoring (U.S. Environmental Protection Agency, 2012a, p., 19–20)......................... 18

Methylmercury Requirements ............................................................................................................................... 18

1. Fish Tissue Sampling .................................................................................................................................... 18

Appendix B. Map of Study Sites ............................................................................................................................... 20

Appendix C. Standard Operating Procedures for Fish Collection and Processing.................................................... 21

Appendix D: Cooperative Monitoring Program.......................................................................................................... 26

Tables

Table 1. Selected data for previous mercury in composite fish tissue samples collected by the U.S. Geological 

Survey in the vicinity of the study area, listed by upstream to downstream sites....................................................... 5

Table 2. Sampling site locations, Boise and Snake Rivers, Idaho, and Brownlee Reservoir, Idaho and Oregon...... 6

Table 3. Sampling site rotation frequency ................................................................................................................. 6

Table 4. Target species anticipated at each sampling site, in order of preference for analysis ................................. 7
iv

Conversion Factors

Multiply By To obtain

Length

inch (in.) 2.54 centimeter (cm)

centimeter (cm) 0.3937 inch (in.)

foot (ft) 0.3048 meter (m)

meter (m) 3.281 foot (ft)

mile (mi) 1.609 kilometer (km)

kilometer (km) 0.6214 mile (mi)

Mass

ounce, avoirdupois (oz) 28.35 gram (g) 

gram (g) 0.03527 ounce, avoirdupois (oz)

gram (g) 0.0001 kilogram (kg) 

gram (g) 1000 milligram (mg) 

Concentration

milligram per kilogram (mg/kg) 1 part-per-million (ppm)

microgram per liter (μg/L) 1 part-per-billion (ppb)

microgram per liter (μg/L) 1000 nanograms per liter (ng/L)

Abbreviations

Abbreviation or 

Acronym Definition

BAF Bioaccumulation factor

CRM Certified reference material

IDEQ Idaho Department of Environmental Quality

IDFG Idaho Department of Fish and Game

NPDES National pollution discharge elimination system

RPTE Reasonable potential to exceed water quality criteria

TMDL Total maximum daily load

USEPA U.S. Environmental Protection Agency

USGS U.S. Geological Survey
1

Monitoring Plan for Mercury in Fish Tissue and Water from 

the Boise River, Snake River, and Brownlee Reservoir, 

Idaho and Oregon 

By Christopher A. Mebane and Dorene E. MacCoy 

Abstract

The methylmercury criterion adopted as a water-quality standard in the State of Idaho is a 

concentration in fish tissue rather than a concentration in water. A plan for monitoring mercury in fish 

tissue and water was developed to evaluate whether fish in the Boise River, Idaho, upstream and 

downstream of wastewater-treatment plant discharges, meet the methylmercury water-quality criterion. 

Monitoring also will be conducted at sites on the Snake River, upstream and downstream of the 

confluence with the Boise River, and in Brownlee Reservoir, which lies along the border between Idaho 

and Oregon. Descriptions of standard procedures for collecting and processing samples and qualityassurance steps are included. This monitoring plan is intended to provide a framework for cooperative 

methylmercury sampling in the lower Boise River basin. 

Background and Objectives

Mercury (Hg) is a global pollutant that ultimately makes its way into every aquatic ecosystem 

through the hydrologic cycle. Atmospheric deposition of inorganic mercury contributes the vast 

majority of mercury to aquatic systems, although geologic sources and point-source pollution also may 

contribute to mercury loading. Once inorganic mercury is in aquatic systems, it may become methylated 

through microbial sulfate reduction (Fitzgerald and Lamborg, 2007). Methylmercury is by far the more 

bioavailable and toxic form of mercury; and, once mercury has moved through aquatic food chains into 

predatory fish, almost all mercury present in fish tissue is methylmercury. In turn, game fish that are 

most commonly caught and eaten in subsistence and recreational fishing tend to be predatory fish. As a 

result of these dynamics, risks of methylmercury exposure to humans are almost exclusively through 

consumption of fish (U.S. Environmental Protection Agency, 2011). 

Mercury is considered to be a neurotoxin to humans, wildlife, and fish. At the molecular level, 

mercury is associated with disruptions in the synthesis of selenocysteine, which is one of the 21 amino 

acids that are essential for all animals. This disruption is related to a cascade of secondary effects from 

the cellular to the whole organism levels. Other adverse effects associated with methylmercury, such as 

ionic homeostasis and reactive oxidative stress, are not obviously linked to selenoprotein inhibition. In 

mammals, including humans, methylmercury has been linked to neurological, cardiovascular, and 

reproductive impairments. The ability of methylmercury to cross the placental barrier and affect the 

nervous system of prenatal infants is of greatest concern (Khan and Wang, 2009). 
2

The linkage between mercury and selenium deficiency leads to observations that selenium 

decreases methylmercury toxicity (Yang and others, 2008; Khan and Wang, 2009). Although much 

recent toxicological evidence points to the intrinsic linkage of mercury and selenium in their relative 

risks to humans, wildlife, and fish, recent fish consumption advisories or criteria for protection of 

human health or the environment have not considered selenium in their assessment of mercury risks 

(U.S. Environmental Protection Agency, 2001; Idaho Department of Environmental Quality, 2005). 

Selenium analyses are not included as a required element of monitoring to determine regulatory 

compliance with methylmercury water-quality criteria in appendix A. However, because (1) the present 

monitoring plan is expected to persist for several years, obtaining data on selenium residues in fish to 

accompany the mercury data might have future value in methylmercury risk assessment, and (2) the 

incremental cost of additional tissue analytes is minor compared to the mobilization and labor costs 

associated with a sampling program, selenium analyses also are included in the present monitoring plan. 

The U.S. Environmental Protection Agency (USEPA) has recommended a water-quality 

criterion for methylmercury that is expressed as a fish tissue residue value (wet-weight methylmercury 

in fish tissue). The Idaho Department of Environmental Quality (IDEQ) adopted the USEPA fish-tissue 

criterion as the State’s methylmercury water-quality criterion and published implementation guidance 

(Idaho Department of Environmental Quality, 2005). The criterion of 0.3 milligrams methylmercury per 

kilogram (mg/kg) of fresh (wet) weight fish is based on protecting an adult consumer who eats an 

average of 17.5 grams of fish per day—about one, 8-ounce meal every other week (U.S. Environmental 

Protection Agency, 2001; Idaho Department of Environmental Quality, 2005). The Idaho 

implementation guidance document describes two scales of monitoring—facility/source monitoring and 

statewide ambient monitoring. Facility monitoring provides information about potential sources of 

mercury, whereas statewide ambient monitoring provides information about impacts of discharges to 

aquatic life that are tied to total maximum daily load (TMDL) and National Pollution Discharge 

Elimination System (NPDES) permitting (Idaho Department of Environmental Quality, 2005). 

However, the statewide ambient monitoring conducted jointly by the U.S. Geological Survey (USGS) 

and IDEQ was discontinued in 2009 due to fiscal constraints. 

The IDEQ guidance document requires NPDES “significant permittees” to provide 

methylmercury in fish tissue data under the reasonable potential to exceed criteria (RPTE) process 

(Idaho Department of Environmental Quality, 2005). The RPTE process is designed to protect human 

health with a fish-tissue methylmercury value not to exceed 80 percent of the 0.3 mg/kg criterion in the 

receiving water body. Potential mercury dischargers to a water body with fish tissue concentrations 

>0.24 mg/kg are considered to have a reasonable potential to exceed criteria. In IDEQ’s implementation 

guidance, municipal dischargers are encouraged to establish monitoring cooperatives to help fund 

watershed-based statewide monitoring for methylmercury in fish tissue. The USEPA further 

recommended that the permitting authority require only one study per water body (U.S. Environmental 

Protection Agency, 2010). The monitoring plan presented here is intended to provide a framework for 

cooperative methylmercury sampling in the lower Boise River basin. A further purpose is to assess 

compliance with the water-quality criterion for mercury to quantify whether the City of Boise’s 

wastewater discharges appreciably influence fish-tissue mercury concentrations in the lower Boise 

River and the Snake River upstream and downstream of the confluence with the Boise River. The data 

also will provide a reference to which future determinations of mercury in fish can be compared.
3

Project Description

To evaluate whether the Idaho methylmercury fish tissue criterion is being met in the lower 

Boise River, the USEPA has included mercury sampling requirements for fish tissue and water in the 

City of Boise’s effluent permits for the Lander Street Wastewater Treatment Plant and the West Boise 

Wastewater Treatment Plant (U.S. Environmental Protection Agency, 2012a, 2012b). The requirements 

specify that a monitoring plan be written and submitted for approval by USEPA and IDEQ within 1 year 

of the effective date of the permit. The effective dates of the City’s permits are May 1, 2012, through 

April 30, 2017. The fish-tissue monitoring components of the permits are appended in full in appendix 

A of this plan and summarized here: 

1. Establish six fish-tissue monitoring stations at locations on the Boise River upstream and 

downstream of the City of Boise wastewater-treatment plants, near the mouth of the Boise River, 

on the Snake River upstream and downstream of the confluence of the Boise River, and one site 

in Brownlee Reservoir. 

2. Develop a sampling plan that specifies sample target species; sample number and size; timing of 

sample collection; and all essential fish collection, handling, and shipping information for field 

sampling teams collecting fish. The plan should include a project description, detailed standard 

operating procedures (SOPs) for fish collection, and instructions for completing field forms and 

labels and for shipping fish samples. Protocols should be consistent with Chapter 4 of 

Implementation Guidance for the Idaho Mercury Water Quality Criteria (Idaho Department of 

Environmental Quality, 2005). 

3. Establish sampling frequency required by the permits to begin within 2 years of May 1, 2012. 

The monitoring will include three cycles of biennial sampling of five sites, with annual sampling 

of one site. 

4. Present protocols used for preparation of samples and analytical methods and for qualityassurance and quality-control techniques. 

5. At each sample location where fish are collected, a surface-water sample must be collected and 

analyzed for total mercury. 

Due to irrigation practices in the lower Boise River basin, fish-tissue sampling is not practical 

during high flows (May–September). The USGS has conducted previous sampling on the lower Boise 

River for community assessment and tissue sampling between October 1 and November 30, depending 

on water levels that, in turn, depend on reservoir and canal operations. 

The U.S. Environmental Protection Agency (2012a, 2012b) wastewater discharge permits also 

call for collecting surface-water samples at each location where fish are collected (appendix A). These 

water samples are to be processed and analyzed for total mercury in water using an analytical method 

that achieves a minimum level of 0.5 ng/L (0.0005 μg/L). 

The implicit purpose of collecting data on mercury in water and fish tissue at the same location 

is to facilitate developing fish bioaccumulation factors, which are ratios of tissue and water mercury 

concentrations. Bioaccumulation factors (BAFs) can be useful for water-quality management, such as 

site-specific implementation targets of the fish-tissue based methylmercury water-quality criteria, and 

TMDL target development (Idaho Department of Environmental Quality, 2005; U.S. Environmental 

Protection Agency, 2010). For developing BAFs, it is not essential that the water and fish samples are 

collected at the same time. Riva-Murray and others (2012) reported that, in streams in Oregon and New 

York, the best BAF estimates came from sampling methylmercury in water during the July to 

September growing season, regardless of when the fish were collected. In related analyses with fish, the 
4

optimal approach for estimating BAFs is to use mercury concentration data from at least 10 adult fish of 

a single species and similar length (Barbara Scudder Eikenberry, U.S. Geological Survey, written 

commun., 2013). 

This monitoring plan is written as if the sampling and analysis methods would all be undertaken 

by USGS personnel. This is not necessarily the case for a project expected to last more than 10 years. 

The intent is that the substantive elements of the sampling could be undertaken by any knowledgeable 

personnel and that the laboratory analyses could be completed by any qualified analytical laboratory that 

was proficient with comparable methods to those described here.

Monitoring Locations and Frequency

Recent fish-tissue mercury data obtained from within the study area provide background 

information on the fish species expected at different locations and their tissue mercury concentrations 

(table 1).

The primary locations planned for collecting fish-tissue samples are listed in table 2. These 

locations were selected because they were within the broad “upstream of, downstream of” reaches 

specified by USEPA’s permits (appendix A). The USGS also has conducted electrofishing at these 

locations; thus, some background information on site access and sampling safety is available. Appendix 

B provides a detailed map of sample sites and their landscape settings.

Sampling must begin in autumn 2013 to meet the deadline outlined in appendix A (within 2 

years following May 2012). One site, the Boise River near Middleton, Idaho, downstream of both the 

Lander and the West Boise Wastewater Treatment Plants, will be sampled each year. The five other 

Boise River, Snake River, and Brownlee Reservoir sites will be sampled every other year. The 

frequency of monitoring will follow the rotation listed in table 3.

Target Species

The fish species to be targeted in this monitoring plan are listed in table 4. The selection of target 

species was based on both the Idaho Department of Environmental Quality (2005) recommendation that 

fish tissue samples should represent the mercury exposures likely encountered from recreational or 

subsistence fishing and on the results of previous fish sampling at these locations (table 1; Clark and 

Maret, 1998; Richter, 2003; MacCoy, 2006). The goal is to collect 10 harvestable-size fish of a target 

species for individual mercury analysis. Harvestable-size fish are considered to be those fish larger than 

the minimum lengths for harvest as established by the Idaho Department of Fish and Game (IDFG); or, 

for fish species without regulatory size limits, individuals greater than 25 cm in length. As of 2013, the 

minimum harvestable size for smallmouth bass in southwestern Idaho is 12 inches (Idaho Fish and 

Game, 2013). Thus, for smallmouth bass, the goal will be to collect fish greater than 30 cm in length, 

rounding to the nearest whole centimeter. 

Actually collecting targeted fish species is an inherently uncertain undertaking because species 

that are common at a location during one sampling event may be scarce or not found during a 

subsequent event. For making comparisons among sites and over time, it is best to collect samples of 

similarly sized fish of the same species. However, the inherent variability of fish distribution may make 

this difficult. Therefore, the sampling crew leader likely will need to make decisions in the field 

regarding retaining alternate species to only those specified in table 4, retaining 10 harvestable-sized 

individuals of different species, or moving to another location within the same water-quality reach 

described in table 2. 
5

Table 1. Selected data for previous mercury in composite fish tissue samples collected by the U.S. Geological 

Survey in the vicinity of the study area, listed by upstream to downstream sites. 

[Data sources: 1997 data are from Clark and Maret (1998); Idaho Department of Fish and Game Nampa 

Hatchery values are from T. Maret, U.S. Geological Survey, unpublished data; other data are from 

http://waterdata.usgs.gov/nwis. 

All mercury values are as total mercury; mg, milligram; kg, kilogram; NR, not reported] 

USGS site 

identification Site name

Year 

sampled

Species (number analyzed, if specified) Tissue

Mean 

mercury (mg/kg wet 

weight) 

Tissue 

moisture 

(percent 

water)

13185000 Boise River near

Twin Springs, Idaho

1997 Largescale sucker (7) Liver 0.23 74

13203760 Boise River at 

Eckert Road near

Boise, Idaho

2011 Mountain whitefish 

(10)

Fillet 0.15 75.5

13210050 Boise River near

Middleton, Idaho

2011 Mountain whitefish 

(10)

Fillet 0.15 76.5

13213030 Boise River at 

Mouth near Parma,

Idaho

2011 Channel catfish

(10)

Fillet 0.23 79.8

13213030 Boise River at 

mouth near Parma,

Idaho

1996 Largescale sucker Liver <0.024 76

13172500 Snake River near

Murphy, Oregon

2004 Channel catfish

(10)

Fillet 0.22 79

13213100 Snake River near

Nyssa, Oregon

1997 Channel catfish (8) Fillet 0.21 77

13213100 Snake River near

Nyssa, Oregon

2006 Channel catfish

(10)

Fillet 0.22 NR

4422221171355 Brownlee Reservoir 

at Burnt River, 

Oregon

1997 Smallmouth bass (6) Fillet 0.29 79

4422221171355 Brownlee Reservoir 

at Burnt River, 

Oregon

1997 White crappie (5) Fillet 0.27 79

4422221171355 Brownlee Reservoir 

at Burnt River, 

Oregon

1997 Channel catfish (7) Fillet 0.35 75

13211387 IDFG Nampa Fish 

Hatchery (hatchery 

reference)

2008 Rainbow trout (5) Fillet 0.012 75

Because the genesis of this study plan was to evaluate whether the City of Boise’s wastewater 

discharges contribute to an appreciable increase in fish methylmercury concentrations in the lower 

Boise River, a further target species goal is to collect the same species upstream and downstream of the 

City of Boise’s discharges (table 4, sites 1 and 2). If this is not accomplished during the initial sampling 

event, the sampling locations should be re-evaluated. 
6

Table 2. Sampling site locations, Boise and Snake Rivers, Idaho, and Brownlee Reservoir, Idaho and Oregon. 

[USEPA - U.S. Environmental Protection Agency; RM – approximate river mile upstream of the river 

mouth. 

The sampling reaches for boat electrofishing may be up to about a kilometer, and the coordinates are for 

the approximate center of reach. The coordinates listed in this table may not be identical to the 

coordinates listed for these sites in NWIS, which usually reflect transects for measuring discharge and 

or collecting water samples http://waterdata.usgs.gov. Coordinates listed in this table are based on 

WGS84] 

Study 

site No.

USGS site 

identification

Site name, river mile (RM), and corresponding 

water 

quality reach descriptions from the USEPA

requirements (appendix A)

North Latitude/West 

Longitude

1 13203760 Boise River at Eckert Road near Boise, Idaho, RM 58 

(“upstream of River Mile 50 in the Lower Boise River”)

43°34'07"N, 116° 08'2.04"W

2 13210050 Boise River near Middleton, Idaho, RM 29

(“an area downstream of both of the City of Boise outfalls 

and near the middle of the Lower Boise River”)

43°41'04"N, 116°34'28"W

3 13213030 Boise River at Mouth near Parma, Idaho, RM 2

(“near the mouth of the Boise River”)

43°47'52"N, 116°59'41"W

4 13172500 Snake River near Murphy, Idaho, RM 454 (“Snake River 

upstream of the confluence of the Boise and Snake 

Rivers”)

43°17'31"N, 116°25'12"W

5 13213100 Snake River near Nyssa, Oregon, RM 385 (“Snake River 

downstream of the confluence of the Boise and Snake 

Rivers”)

43°52'34"N, 116°58'57"W

6 4422221171355 Snake River (Brownlee Reservoir) at Burnt River, Oregon, 

RM 328 (“within the Brownlee Reservoir”)

44°22'22"N, 117°13'55"W

Table 3. Sampling site rotation frequency. 

[Study site numbers from table 2. Time of year is for Boise River and Snake River sampling. Brownlee 

Reservoir sampling may be conducted at different times of the year than other sampling because of 

safety, coordination with other efforts, to target spring spawning fish aggregations, or other logistical 

reasons]

Year Time of year

Study sites to be 

sampled

2013 October–November 1, 2, 3, 4, 5, 6

2014 October–November 2

2015 October–November 1, 2, 3, 4, 5, 6

2016 October–November 2

2017 October–November 1, 2, 3, 4, 5, 6

2018 October–November 2
7

Year Time of year

Study sites to be 

sampled

2019 October–November 2

2020 October–November 2

2021 October–November 2

2022 October–November 1, 2, 3, 4, 5, 6

Table 4. Target species anticipated at each sampling site, in order of preference for analysis. 

[IDFG, Idaho Department of Fish and Game] 

Study 

site No. Site name Expected species

1 Boise River at Eckert Road near Boise, Idaho Mountain Whitefish, Brown Trout, Rainbow Trout

2 Boise River near Middleton, Idaho Mountain Whitefish, Brown trout, Largemouth Bass, 

Smallmouth Bass

3 Boise River at mouth near Parma, Idaho Mountain Whitefish, Largemouth Bass, Smallmouth 

Bass, Channel Catfish

4 Snake River near Murphy, Idaho Smallmouth Bass, Largemouth Bass, Channel Catfish

5 Snake River near Nyssa, Oregon Smallmouth Bass, Mountain Whitefish, Largemouth 

Bass, Channel Catfish

6 Brownlee Reservoir near Burnt River, Oregon Smallmouth Bass, Crappie spp., Largemouth Bass, 

Channel Catfish

Fish collected will be kept in a live well on the boat until they can be weighed and measured. If 

fewer than 10 harvestable-sized individuals of any game fish species (listed in table 4 or others listed by 

the IDFG in their annual fishing regulations) can be captured with sufficient effort (defined as a single 

sampling day for a site), then whatever numbers of harvestable game fish captured will be processed 

and analyzed. In the event that sampling is compromised, interrupted, or inefficient owing to difficulties 

such as equipment problems, or if weather or site conditions prevent sampling, additional sampling 

efforts will be made to collect an adequate sample. 

Data-Quality Objectives

The principal data-quality objectives of this sampling and analysis were specified by the U.S. 

Environmental Protection Agency (2012a, 2012b): 

“The objective of the Methylmercury Fish Tissue Monitoring program is to collect reliable 

methylmercury fish tissue data, within a specific geographic area, to determine if fish tissue 

concentrations of methylmercury are compliant with Idaho’s methylmercury fish tissue criterion of 

0.3 mg/kg. The monitoring program may also be used to advise the public on safe levels of fish 

consumption.” 

More specific objectives toward meeting those goals include:

1. Fish collections will be designed to collect fish tissue that would be reasonably 

representative of fish and size ranges likely to be caught and eaten by recreational or 

subsistence anglers in the vicinity of sampling locations;
8

2. Sample processing, handling, storing, and shipping to the laboratory will use sufficient 

quality-assurance measures to avoid introducing sample contamination or bias to the data; 

3. Laboratory analytical techniques will be used that have sufficiently low detection limits to 

quantify Hg levels in fish tissue at less than 0.24 mg/kg wet weight. [The expected 

laboratory quantification limit for the fish-tissue samples is about 0.005 mg/kg (see section, 

“Laboratory Methods”)]. 

4. Laboratory analytical techniques will be used that have sufficiently low detection limits to 

quantify Hg levels in water at 0.5 ng/L. 

5. Laboratory analytical techniques will use and report sufficient quality-assurance and control 

steps that the accuracy and precision of the data reported will be known. The accuracy of the 

data should be within 20 percent of the most probable value for certified reference materials 

for mercury in fish tissues, and the precision (repeatability) of the data should be within 20 

percent relative percent difference in laboratory replicate analyses. 

6. Following review, data will be made available to the public and environmental management 

agencies through an online database and by periodic data reports. 

Field Sampling and Sample Processing

Safety and Crew Training

Although the safety of sampling personnel and bystanders is always a priority during field work, 

fish collection by boat electrofishing in non-wadeable, flowing water poses real risks of death or injury 

by electrocution, drowning, or hypothermia. Therefore, appropriate crew training and attention to safety 

are essential for boat electrofishing. Although it is not feasible to specify all safety precautions in this 

plan, some key points taken from Meador and Cuffney (1993) and Temple and Pearsons (2007) bear 

emphasis. 

At least one designated crew leader will have received formal training in the principles and 

safety of electrofishing within 5 years of the sampling event. In addition, crew members will have prior, 

practical experience in electrofishing and river safety. The training should be acquired through an 

authoritative source, such as that offered by electrofishing equipment manufacturers. The U.S. Fish and 

Wildlife Service’s National Conservation Training Center (http://nctc.fws.gov/) also provides 

electrofishing training courses. Before electrofishing begins, the crew leader will be responsible for 

briefing all crew members on safety precautions. 

Maneuvering a boat or raft in a river channel brings inherent risks of capsize or throwing crew 

members overboard from striking hazards, such as rocks, rubble, rebar, or other debris; becoming 

entrained in sweepers from downed trees; getting snagged on fencing or tangled in low hanging tree 

branches; or entrapping feet. Boat work in large waters, such as the Snake River and Brownlee 

Reservoir in cold weather brings added hazards of hypothermia and swamping from wind waves. These 

hazards are more acute for an electrofishing crew than for routine recreational boating because of the 

crew’s attention to the operation of the electrofishing unit and spotting and netting fish. Therefore, it is 

essential that the crew leader is experienced in boat handling, conservative, and does not take avoidable 

risks. All crew members are responsible for remaining aware of their situation and looking ahead for 

hazards. 

Sampling in the Boise and Snake Rivers will be conducted during periods of low flows, typically

October or November, to reduce hazards from maneuvering the boat or raft in high water velocities. 

Although sampling usually can proceed in mild drizzle or light rain, heavy rain should halt operations. 
9

The timing of sampling on Brownlee Reservoir might vary from the river sampling for safety, 

coordination with other sampling efforts, or to target spawning aggregations. Winds and dangerous 

waves can come up quickly on a reservoir with a long fetch, such as Brownlee Reservoir. Reservoir 

sampling and transit will be limited to littoral areas within about 50 m from shore. Insulated float coats 

that meet U.S. Coast Guard requirements for a Type III personal flotation device (PFD) are 

recommended in lieu of non-insulated floatation devices for cold-weather river work. 
10

Although electrofishing has been in use for more than 100 years, the application of electricity 

into water to capture fish is inherently dangerous work, and the voltage and amperage produced by boat 

electrofishing units is sufficient to electrocute workers (Meador and Cuffney, 1993). Precautions include 

wearing neoprene waders, rubber lineman-type gloves, and PFDs. Only dipnets with nonconductive 

fiberglass shafts may be used. The kill switch for the electrofishing unit must be attached to the bow 

netter, so that if the netter falls overboard, the electrical current will automatically be shut off. 

Electrofishing may attract interested bystanders. One crew member should remain onshore and 

be dedicated to ensuring the safety of bystanders, especially the need to keep children or dogs well clear 

of the water. A flyer, written in English and Spanish, explaining the purpose and hazards of the 

sampling would be beneficial to have on hand. If bystanders are likely to be present, dedicating one 

crew member to public interaction can ensure safety, improve the experience for the public, and allow 

the other crew members to continue their work without excessive distraction. However, if bystanders do 

not heed admonitions to stay clear of the water during electrofishing, the sampling must be interrupted. 

If so, the sampling crew may need to move to a different site or finish sampling at another time.

This summary of some precautions is by no means exhaustive, and is no substitute for actual 

training and experience. Communication, caution, and situational awareness are essential. 

Permits and Coordination

Fish-tissue sample collection requires an Idaho Scientific Collection Permit, which may be 

granted by IDFG. The permit application is specific to the individual permittee conducting the sampling 

and to sub-permittees who are qualified to collect in the absence of the permit holder. The permit 

application also is specific to gear types and to sampling locations. Permit applications must be filed at 

least 6 weeks prior to planned sampling (http://fishandgame.idaho.gov/public/licenses/). The list of 

requested sampling locations must be flexible enough to allow for moving the planned sample locations 

within the general “upstream and downstream of” monitoring reaches listed in appendix A. Sample 

locations may need to be moved for the safety of sampling personnel or bystanders, or in the event that

fishing is poor at a targeted location, or for other operational reasons. For the Brownlee Reservoir 

samples, any site within the reservoir will be considered to be an acceptable monitoring location. A 

boat-mounted electrofisher is the preferred method of capture in rivers and near the shoreline in the 

reservoir, as it involves minimal handling of fish. However, boat electrofishing may not be effective in 

deep water or for large fish. Therefore, alternate methods, such as gill nets, seines, or hook and line, also 

should be sought for inclusion in the Idaho Scientific Collection Permit. 

Standard Procedures for Sample Collection and Processing

In brief, the procedures for fish sample collection will be as follows: 

1. Fish will be collected by electrofishing or alternative permitted methods, and all fish that 

are eligible for analysis will be retained, alive, in the live well of the boat. This includes 

all targeted species (table 4) or any fish classified as a game fish by IDFG; 

2. When the crew measures the fish, the first 10 fish of the target species listed in table 4 or 

alternate species, that are greater than 25 cm in length, (except smallmouth bass, which 

must be greater than 30 cm), may be retained for samples. 
11

3. If enough individuals of the targeted species are not captured within the expected level of 

effort (one sampling day), then a mixed catch of different species is acceptable. In this 

event, the crew also will retain samples of any other species listed in table 4 such that a 

total of 10 game fish greater than 25 cm in length, or for smallmouth bass, greater than 

30 cm, were retained; 

4. If fewer than 10 individuals of any target fish species greater than 25 cm in length can be 

caught, then all captured target fish greater than 25 cm in length, or for smallmouth bass, 

greater than 30 cm, will be retained and processed. All other fish will be released alive, 

unless specified otherwise in the scientific collection permit.

5. Fish will be individually placed in clean, clear, zip-seal bags on wet ice and returned to 

the sample preparation area. Fish will be kept on ice and processed within 24 hours to 

minimize possible loss of sample integrity. 

6. Two skinless fillets will be obtained from each fish. One fillet is intended for primary 

mercury analyses, and the second fillet will be retained frozen as a backup sample. 

Because the subsamples for selenium will only require about 25 mL of tissue, there will 

be remaining tissue from the second fillets. The remainder should be retained as a backup 

sample for up to 6 months (or at least until data reviews are completed) in the event that 

additional analyses are desired, as a precaution against shipping or other sample mishaps, 

and as an archive for analytical reruns, if needed. 

7. Shipping will be by traceable, overnight delivery service. 

More specific details for sample processing are provided in appendix C, which was largely taken 

from Scudder and others (2008, p. 9-18), following their steps for “Top Predator Fish.” 

Water samples for analysis will be collected from the same locations as the fish samples, but not 

necessarily at the same times. If not collected concurrently with the fish samples, the water samples will 

be collected during the July to September growing season. Water samples will be collected as dip 

samples for unfiltered, total mercury (UTHg) following the collecting and handling techniques of Lewis 

and Brigham (2004), or by the functionally similar techniques described by Essig (2010). In short, the 

technique uses a “clean hands/dirty hands” approach in which one person with clean, powderless gloves 

handles the sample bottles and the “dirty hands” person assists the clean-hands person by helping them 

with gloves, opening and sealing bags, and so on. Dip samples will be collected in 500-mL precleaned 

fluoropolymer or fluorocarbon polymer (FP) bottles. Precleaned FP bottles will be triple-rinsed with the 

water to be sampled, filled to the shoulder to allow space for preservative, and capped. Samples will be 

preserved with 10 mL of 6 N ultra-trace hydrochloric acid. Quality-control samples will include at least 

one field blank per sampling round. A field blank is reagent water that has been transported to the 

sampling site and exposed to the same equipment and operations as a sample at the sampling site, a 

procedure defined by Wilde (2006, at section 4.3 “Quality-Control Samples”). Full details on field 

sampling methods are given by Lewis and Brigham (2004). 
12

Laboratory Methods

Mercury

Biological Total Mercury in Fish Tissue

Although the permit requirements describe a “Methylmercury Fish Tissue Monitoring Program,” 

the laboratory analyses will be for total mercury in fish tissue rather than for methylmercury. This is for 

two reasons: (1) total mercury is easier and less costly for laboratories to determine than is 

methylmercury, and (2) nearly all mercury present in fish muscle tissue is methylmercury (Bloom, 

1992; Hammerschmidt and others, 1999; Harris and others, 2003). Interpretation of total mercury 

analysis as methylmercury will likely bias high the results as methylmercury in fish on the order of 

factors of <1.01 to 1.05 based on comparisons shown by Bloom (1992) and by Hammerschmidt and 

others (1999). This magnitude of potential bias is well within the range of expected analytical 

variability. In comparing the fish tissue results with the criterion, the analytical results for total mercury 

in the fish tissue will be interpreted as 100 percent methylmercury.

Analyses of total mercury in fish tissue are planned to be conducted through the USGS Mercury 

Research Laboratory (USGS MRL), 8505 Research Way, Middleton, Wisconsin, 53562, (608) 821-

3844, http://wi.water.usgs.gov/mercury-lab/. For “biological total mercury” analyses (that is, of total 

mercury in fish tissue), the laboratory will provide analyses consistent with USEPA Method 7473 for 

“Mercury in solids and solutions by thermal decomposition, amalgamation, and atomic absorption 

spectrophotometry” (U.S. Environmental Protection Agency, 2007). 

The biological total mercury method provides a nominal detection limit (minimum level) of 

5 ng/g (0.005 mg/kg) dry weight, based on a 20–50 mg sample size. The USGS MRL acceptance

criteria for reported data include an acceptable percent recovery on a certified reference material within

±15 percent of the theoretical value, which is more stringent than the overall data acceptance criteria for 

this overall plan in section, “Data-Quality Objectives.” Certified reference materials (CRMs) may 

include those from the National Research Council Canada dogfish liver certified reference material for 

trace metals or other biological tissues depending on availability, and/or the National Institute of 

Standards and Technology (NIST) Lake Superior or Lake Michigan fish tissue standard reference 

materials.

The system or method blanks are used to determine the actual detection limits achieved (3X the 

standard deviation of blanks as mass, then divided by the mass of sample analyzed), which results in the 

actual detection limits achieved varying sample to sample from the nominal detection limit. The USGS 

MRL analyzes one sample in triplicate for every 10 samples analyzed, in addition to two system blanks 

and one CRM. The relative standard deviation of the triplicate analyses (RSD, calculated as the standard 

deviation/average) should be within 15 percent (John DeWild, USGS Mercury Research Laboratory, 

written comm., December 5, 2012). Further details of data-quality measures used at the USGS MRL are

available online at http://wi.water.usgs.gov/mercury-lab/index.html. 
13

As this fish tissue monitoring project matures, different laboratories may be considered for use, 

depending on factors, such as capacity at the USGS MRL or for the convenience of analyzing both 

mercury and selenium samples at a single laboratory. Any different laboratories used must meet the 

data-quality objectives specified herein. 

Total Mercury in Water

Unfiltered water samples will be analyzed for total mercury using laboratory methods consistent 

with USEPA Method 1631 (U.S. Environmental Protection Agency, 2002). This method is expected to 

provide a nominal minimum level of 0.5 ng/L (0.0005 μg/L). Quality-control acceptance criteria for 

total mercury in water include matrix spikes to determine ongoing precision and recovery, with 

recoveries within 77 to 123 percent of the theoretical value. The relative percent difference of matrix 

spike duplicates must be less than 25 percent (U.S. Environmental Protection Agency, 2002). The 

primary laboratory for the analyses of total mercury in water is anticipated to be the Boise City Water 

Quality Laboratory, 11818 Joplin Road, Boise, Idaho, 83714. As a contingency, analyses of total 

mercury in water also may be obtained from Brooks Rand LTD, 3950 Sixth Avenue NW, Seattle, 

Washington, 98107. 

Selenium in Fish Tissue

Because the USGS MRL provides only mercury analyses, analyses for total selenium in fish 

tissue would be handled by a different laboratory. The specific laboratory has not yet been identified, 

but it will be expected to provide analyses using modified USEPA Method 1638 (U.S. Environmental 

Protection Agency, 1996) or alternative methods that provide at least similar performance, such as those 

of Garbarino and others (2006). Laboratories using this method have obtained minimum levels of 0.1 

mg/kg dry weight or less (for example, Essig, 2010). As these analyses are separate from the permit 

prescriptions for 10-each mercury samples given in appendix A, three samples per site should be 

sufficient to provide an average value for fish tissue selenium for each site for the species sampled. 

Quality Assurance and Quality Control

The sampling and analysis will include both quality-assurance and quality-control measures. 

Although the concepts of quality assurance and quality control in water-quality monitoring are 

commonly combined as “QA/QC,” the USGS Water Mission Area distinctly defines quality assurance 

and quality control. Quality assurance procedures control those unmeasurable components of a project, 

such as sampling at the right place with the right equipment and using the right techniques. Quality 

control steps include data generated to estimate the magnitude of the bias and variability in the 

processes for obtaining environmental data.
14

Adherence to standard USGS quality-assurance protocols is mandatory, and quality-control 

procedures are to be incorporated into every water-quality data-collection effort. Quality assurance of 

the data collected includes the timely and accurate documentation of field information in electronic and 

paper records, auditing of such records, consistently and conscientiously using procedures and protocols 

to ensure sample integrity and data quality, and training in measurement techniques and the collection of 

quality-control data (Wilde, 2009). 

Project-specific quality-assurance steps in the field sampling include the use of multiple (10) 

field replicates to ensure that the samples are representative of that species and size of fish present at the 

time of sampling, standard procedures for equipment cleaning, sample collection and processing of the 

field samples, and data reviews. These steps are detailed in their respective sections in this document. 

Quality-control steps include the analyses of replicates and the use of certified or standard reference 

fish-tissue sample materials as described in section, “Laboratory Methods.” 

Reporting

USEPA’s permits require that the results must be reported by March 31 of the year following 

sampling (appendix A). This schedule is feasible if samples can be collected during the July to 

September sampling index period recommended by the Idaho Department of Environmental Quality 

(2005) (that is, with a deadline 6 to 8 months post sampling). However, because reservoir and irrigation 

operations make the Boise River unsafe for electrofishing until October or November annually, this 

March 31 reporting deadline would only allow 4 to 5 months after the anticipated sample collections for 

laboratory analyses, data review, and report preparation. Tissue analyses from the USGS MRL in 

Middleton, Wisconsin may take from 3 to 4 months and subsequent data-quality reviews by the USGS

may take up to 2 months. Thus, if fish tissue samples are collected toward the end of November, the 

final quality-reviewed data may not be available to release online until as late as the end of May and the 

annual report with the final data by the end of June. To meet USEPA’s March 31 reporting deadline 

under these constraints, we anticipate providing an informal, preliminary sampling completion summary 

by March 31 of each year, and, as follows, a final data report by June 30 of each year.

Further, to meet the annual reporting requirements of the City of Boise’s discharge permits (U.S. 

Environmental Protection Agency, 2012a, 2012b), a brief annual report will be provided. For the years 

that seven locations are sampled (table 3), this annual report is expected to be a USGS Data Series

report, which is a brief, citable, non-interpretive, online report. Such a report is expected to also satisfy 

IDFG’s required reporting of the fish actually collected through the Idaho Scientific Collection Permit.

For the alternate years when only a single site is sampled, the annual report will consist of a simple 

electronic letter with an attached data spreadsheet.

Additionally, the laboratory data will be stored electronically in the USGS National Water 

Information System (NWIS), http://nwis.waterdata.usgs.gov/id/nwis/qwdata) database and, following 

review, made publicly available via the NWIS Web Interface. Although this Web address is accurate at 

the time of writing, as the USGS database is updated and integrated with other databases or data 

aggregation services, the details of the online data access may change over time. 
15

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http://dx.doi.org/10.1139/f92-113. 

Clark, G.M., and Maret, T.R., 1998, Organochlorine compounds and trace elements in fish tissue and 

bed sediments in the Lower Snake River Basin, Idaho and Oregon: U.S. Geological Survey WaterResources Investigations Report 98-4103, 35 p. (Also available at

http://pubs.er.usgs.gov/publication/wri984103.) 

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statewide assessment: Boise, Idaho, Idaho Department of Environmental Quality, 64 p. plus 

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arsenic_mercury_fish_tissue_report_0310.pdf. 

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H.D., and Turekian, K.K., eds., Treatise on Geochemistry: Oxford, Pergamon Press, chap. 9.04, p. 1-

47, http://dx.doi.org/10.1016/B0-08-043751-6/09048-4. 

Garbarino, J.R., Kanagy, L.K., and Cree, M.E., 2006, Determination of elements in natural-water, biota, 

sediment, and soil samples using collison/reaction cell inductively coupled plasma—Mass 

Spectrometry: U.S. Geological Survey Techniques and Methods, book 5, chap. B1, 88 p.. (Also 

available at http://pubs.usgs.gov/tm/2006/tm5b1/.) 

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eggs in yellow perch related to maternal exposure in four Wisconsin lakes: Environmental Science 

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Harris, H.H., Pickering, I.J., and George, G.N., 2003, The chemical form of mercury in fish: Science, v. 

301, no. 5637, p. 1,203, http://dx.doi.org/10.1126/science.1085941. 

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Water Quality Criteria: Boise, ID, Idaho Department of Environmental Quality, 212 p., accessed 

September 5, 2013, athttp://www.deq.state.id.us/water-quality/surface-water/mercury.aspx. . 

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2013, at http://fishandgame.idaho.gov/public/fish/rules/. 

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toward a molecular understanding of the mercury–selenium antagonism: Environmental Toxicology 

and Chemistry, v. 28, no. 8, p. 1,567-1,577. 

Lewis, M.E., and Brigham, M.E., 2004, Low-level mercury, in Wilde, F.D., Radtke, D.B., Gibs, J., and 

Iwatsubo, R.T., eds., Chapter A5 Processing of Water Samples: National Field Manual for the 

Collection of Water-Quality Data: U.S. Geological Survey Techniques of Water-Resources 

Investigations, book 9, accessed December 2012, at http://pubs.water.usgs.gov/twri9A5/. 

MacCoy, D.E., 2006, Fish communities and related environmental conditions of the lower Boise River, 

southwestern Idaho, 1974–2004: U.S. Geological Survey Scientific Investigations Report 2006-5111, 

36 p. (Also available at http://pubs.usgs.gov/sir/2006/5111/.) 

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September 5, 2013, at http://water.usgs.gov/nawqa/protocols/OFR-93-104/. 
16

Moulton, S.R., II, Kennen, J.G., Goldstein, R.M., and Hambrook, J.A., 2002, Revised protocols for 

sampling algal, invertebrate, and fish communities as part of the National Water-Quality Assessment 

Program: U.S. Geological Survey Open-File Report 02-150, 75 p. (Also available at 

http://pubs.usgs.gov/of/2002/ofr-02-150/index.html.). 

Richter, T.J., and Chandler, J.A., 2001, Water-level impacts to spawning smallmouth bass, crappie spp., 

and channel catfish in Richter, T.J., ed., Hells Canyon Complex Resident Fish Study, revised 2003: 

Boise, Idaho, Idaho Power Company, 76 p., accessed September 5, 2013, at 

http://www.idahopower.com/pdfs/Relicensing/hellscanyon/hellspdfs/techappendices/Aquatic/e31_05_

ch01.pdf. 

Riva-Murray, K., Bradley, P.M., Scudder Eikenberry, B.C., Knightes, C.D., Journey, C.A., Brigham, 

M.E., and Button, D.T., 2012, Optimizing stream water mercury sampling for calculation of fish 

bioaccumulation factors: Environmental Science & Technology, v. 47, no. 11, p. 5904–5912, 

http://dx.doi.org/10.1021/es303758e. 

Scudder, B.C., Chasar, L.C., DeWeese, L.R., Brigham, M.E., Wentz, D.A., and Brumbaugh, W.G., 

2008, Procedures for collecting and processing aquatic invertebrates and fish for analysis of mercury 

as part of the National Water-Quality Assessment Program: U.S. Geological Survey Open-File Report 

2008-1208, 34 p. (Also available at http://pubs.usgs.gov/of/2008/1208/.) 

Temple, G.N., and Pearsons, T.N., 2007, Electrofishing: Backpack and drift boat, in Johnson, D.H., 

Shrier, B.M., O'Neal, J., Knutzen, J.A., Xanthippe, A., O'Neill, T.A., and Pearsons, T.N., eds., 

Salmonid field protocols handbook: Techniques for assessing status and trends in salmon and trout 

populations: Bethesda, Maryland, American Fisheries Society, p. 95–132.U.S. Environmental 

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plasma — Mass Spectrometry: U.S. Environmental Protection Agency, EPA Method 1638 (SW-846), 

50 p. 

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health: methylmercury: Washington, DC, U.S. Environmental Protection Agency, EPA-823-R-01-

001, 303 p., accessed September 5, 2013, at 

http://www.epa.gov/waterscience/criteria/methylmercury/. 

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water by oxidation, purge and trap, and cold vapor atomic fluorescence spectrometry: Washington, 

D.C., U.S. Environmental Protection Agency, Office of Water, EPA-821-R-02-019, 46 p., accessed 

September 5, 2013, at http://water.epa.gov/scitech/methods/cwa/metals/mercury/index.cfm. 

U.S. Environmental Protection Agency, 2007, Mercury in solids and solutions by thermal 

decomposition, amalgamation, and atomic absorption spectrophotometry: U.S. Environmental 

Protection Agency, EPA Method 7473 (SW-846), accessed September 5, 2013, at 

www.epa.gov/osw/hazard/testmethods/sw846/pdfs/7473.pdf. 

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methylmercury water quality criteria: U.S. Environmental Protection Agency, EPA-823-R-10-001. 

221 p., accessed September 5, 2013, at http://www.epa.gov/waterscience/criteria/methylmercury/. 

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Discharge Elimination System: Lander Street Wastewater Treatment Facility, City of Boise: U.S. 

Environmental Protection Agency, Permit No.: ID-002044-3, 53 p., accessed September 5, 2013, at 

http://yosemite.epa.gov/r10/water.nsf/NPDES+Permits/Current+ID1319. 
17

U.S. Environmental Protection Agency, 2012b, Authorization to discharge under the National Pollutant 

Discharge Elimination System: West Boise Wastewater Treatment Facility, City of Boise: U.S. 

Environmental Protection Agency, Permit No.: ID-002044-3, 52 p., accessed September 6, 2013, at 

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http://water.usgs.gov/owq/FieldManual/chapter4/html/Ch4_contents.html. 

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Techniques of Water-Resources Investigations, book 9, chap A6 (v. 2.2), (Also available at 

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Interactions and mechanisms: Environmental Reviews, v. 16, p. 71-92, http://dx.doi.org/10.1139/A08-

001. 
18

Appendix A. Excerpt of U.S. Environmental Protection Agency Permit No.: ID002398-1 Requirements for Methylmercury Fish Tissue Monitoring (U.S. 

Environmental Protection Agency, 2012a, p., 19–20)

Methylmercury Requirements

1. Fish Tissue Sampling

Objective: The objective of the Methylmercury Fish Tissue Monitoring program is to collect 

reliable methylmercury fish tissue data, within a specific geographic area, to determine if fish tissue 

concentrations of methylmercury are compliant with Idaho’s methylmercury fish tissue criterion of 0.3 

mg/kg. The monitoring program may also be used to advise the public on safe levels of fish 

consumption. 

Applicability: The permittee may satisfy the requirements of the Methylmercury Fish Tissue 

Monitoring Program by arranging to participate in a cooperative effort with other entities which have 

NPDES permitted discharges to the Lower Boise River or tributaries to the Lower Boise River. 

Requirements: The permittee must develop and submit a Methylmercury Fish Tissue 

Monitoring Plan to the Director of the Office of Water and Watersheds and the IDEQ for review and 

approval within one year of the effective date of the permit. At a minimum the plan must include the 

following elements:

• Identify all participants (e.g., City of Boise, other municipalities or industries) funding the 

monitoring program. The monitoring plan must be updated each time a municipality or industrial 

facility joins the cooperative monitoring program, and the City of Boise must provide notice to the 

USEPA and the IDEQ each time a new entity becomes part of the cooperative monitoring program. 

Written notice must be provided to the USEPA and the IDEQ within 30 days of a new participant 

joining the program. 

• Monitoring stations where fish tissue samples will be collected. One monitoring station must be 

located in each of the following areas: 

• Upstream of River Mile 50 in the Lower Boise River 

• An area downstream of both of the City of Boise outfalls and near the middle of the Lower 

Boise River

• Near the mouth of the Boise River

• Snake River upstream of the confluence of the Boise and Snake Rivers 

• Snake River downstream of the confluence of the Boise and Snake Rivers 

• Within the Brownlee Reservoir 

• Name, address of organization collecting and analyzing fish tissue samples. The organization 

must have experience in the collection and analysis of methylmercury fish tissue samples.
19

• Develop a sampling plan that specifies sample target species, sample number and size, timing of 

sample collection, and all essential fish collection, handling, and shipping information for field 

sampling teams collecting fish. The plan should include a project description, detailed standard 

operating procedures (SOPs) for fish collection, and instructions for completing field forms and 

labels and for shipping fish samples. Protocols should be consistent with Chapter 4 of 

Implementation Guidance for the Idaho Mercury Water Quality Criteria (Idaho Department of 

Environmental Quality, 2005). 

• Identify all protocols related to sample preparation methods and analytical methods to be used on 

samples.

• Identify data quality goals for all sample collection and handling activities and describe the Quality 

Assurance/Quality Control (QA/QC) techniques employed by field teams to support those goals. 

Sample Frequency: Initial sampling must occur within 2 years of the effective date of the 

permit. Following the initial sampling event monitoring must occur at least once every two years from 

five of six sample locations, and yearly at the sixth location. After three sampling cycles, five of the six 

sample locations should be sampled once every 5 years. Sample sites will be determined in consultation 

with IDEQ.

Additional Sampling: At each sample location where fish are collected a surface water sample 

must be collected and analyzed for total mercury using an analytical method which achieves a Minimum 

Level of 0.0005 μg/L. 

Reporting Requirements: The permittee must submit a report which lists the participants 

financing the monitoring program; the name, address and phone number of the entity collecting and 

analyzing samples; sample locations; target species used; sample size; time samples were collected; 

analytical methods used; results, and any other information relevant to the monitoring program. The 

permittee must submit the report to the USEPA, the IDEQ and the Idaho Fish Consumption Advisory 

Board by March 31st of the year following sampling. 

Revision to the Methylmercury Monitoring Plan: Any revisions to the Methylmercury 

Monitoring Plan must be approved by the IDEQ and the Director of the Office of Water and 

Watersheds.
20

Appendix B. Map of Study Sites

Appendix B is online only, and consists of a detailed map of sample sites and their landscape 

settings, viewable with the Google Earth application (http://www.google.com/intl/en/earth/index.html) 

or other Internet-based, two-dimensional map and three-dimensional Earth browsers (.kml file). The 

.kml file can be downloaded at http://pubs.usgs.gov/of/2013/1068/. 
21

Appendix C. Standard Operating Procedures for Fish Collection and Processing

The following procedures were excerpted from Scudder and others (2008), omitting some 

internal citations.

Preparation of Equipment and Supplies

Suggested equipment and supplies are listed in appendix 2 of Scudder and others (2008). 

Supplies and equipment that come in contact with organisms should consist of new or clean plastic 

(Teflon®, polypropylene, polyethylene, or polyethylene terephthalate whenever possible). When in 

doubt, consult the USGS MRL in Middleton, Wisconsin regarding container recommendations. Highgrade stainless steel knives may be used for filleting and dissecting fish. 

Prepare assembled equipment and supplies to minimize the potential for sample contamination. 

New, sealed supplies, such as zip-seal plastic bags and plastic vials with plastic caps, do not need precleaning for the purposes described in this biological sampling protocol. Prior to field work, clean all 

other supplies and equipment in a dilute (0.1-percent by volume) solution of non-ionic surfactant 

detergent (Liquinox®) by soaking equipment for 30 minutes and then using a plastic scrub brush to 

scrub all surfaces. Rinse equipment with copious amounts of tap water because residual detergent on 

supplies or equipment could contaminate tissues for stable carbon isotope and other chemical analyses. 

All non-metal equipment (for example, cutting boards, trays, plastic forceps, plastic sieves) should then 

be soaked in 5-percent hydrochloric acid (trace metal grade such as Omni Trace®) for 8 to 24 hours 

prior to initial sampling and triple rinsed in deionized (DI) water (<0.055 μS/cm). Fillet knives and 

other stainless steel tools should not be cleaned with acid; these tools should be cleaned with dilute 

detergent solution, rinsed with copious amounts of tap water, triple rinsed with DI water, and air dried 

completely prior to storage in order to minimize corrosion. Small, high-grade stainless steel disposable 

dissecting knives are an option for processing forage fish. After they are cleaned, supplies and smaller 

equipment should be double-bagged in new, clear plastic bags and stored in sealed containers to 

minimize contamination; supplies should be cleaned and packed separately for each site to minimize the 

need for field cleaning. Large, new, clear plastic bags can be used to wrap nets and other gear so that 

they do not directly contact truck beds or other potentially highly contaminating surfaces. In the field, 

all equipment should be cleaned between sites by scrubbing with dilute Liquinox® and rinsing with 

copious amounts of tap water, triple rinsing with DI water, rinsing with 5-percent hydrochloric acid 

(non-metal items only), and again triple rinsing with DI water.

Preparation and Review of Field Forms and Labels 

Field personnel should preview field forms, sample labels, and laboratory submission forms. See 

section on Field Data Forms and Sample Labels later in this appendix. Examples of completed forms 

and labels are provided by the USGS MRL. Field forms and labels should be preprinted with station 

name, USGS station number, analyte, medium code, and contact information for the project chief 

(name, e-mail, and telephone number). This is not only a valuable time-saving measure for field work 

but an important tool for to minimizing errors on field forms. 
22

Fish Collection

Fish may be collected by any means that do not result in contamination of their tissues for 

chemical analyses. A variety of fish-collection procedures may be appropriate, depending on site 

conditions and target species. General fish-collection procedures are described elsewhere (Meador and 

Cuffney, 1993; Moulton and others, 2002), and rely primarily on electrofishing (backpack, barge, and 

boat). Other methods in combination with or in lieu of electrofishing, such as seining or rod-and-reel 

(with artificial lures), or passive gear, such as traps or nets, may be more effective at some sites and are 

acceptable. After capture, fish should be placed in a live cage/net in the stream (large top predator fish 

only, as small forage fish may be damaged), a large aerated bucket, or an aerated live well to minimize

stress until processing, to keep fish alive, and to allow any unneeded fish to be returned live to the 

stream. Fish can be anesthetized using carbon dioxide from carbon dioxide-producing tablets, such as 

Alka-Seltzer® (2-4 tablets per gallon of water in bucket or other container). After anesthetization, fish 

can be euthanized by additional carbon dioxide or a sharp blow to the base of the skull. If fish are to be 

processed in a location other than where they were collected, place them in clean zip-seal bags on wet 

ice and process them within 24 hours to minimize possible loss of sample integrity. 

Sample Processing

Samples must be processed in a clean environment. Processing at the site, or a nearby outdoor 

area, is acceptable if a stable, clean work area is available. Processing in an enclosed facility, such as a 

field laboratory, also is acceptable. Avoid sources of contamination, such as dusty roads, heavy traffic, 

older field and laboratory vehicles, or older buildings where dust and (or) particle-shedding from 

building materials (for example, paneling, or ceiling tiles) might be of concern. Avoid facilities or 

vehicles where any forms of Hg, including Hg-based preservatives and manometers, have been used. 

Cover all work surfaces with new clear plastic sheeting or bags. Wear disposable, powder-free plastic 

gloves during all sample processing. Change gloves frequently, particularly after touching any unclean 

surface. Clean, thicker reusable plastic gloves, such as dishwashing gloves, may be used for fish 

handling where thinner, disposable gloves would tear upon contact with spines of a fish. For reusable 

gloves, wash outsides thoroughly with detergent solution, tap water, and DI water between sampling 

sites. 

Care should be taken during sample processing and storage to minimize desiccation as fish 

contain approximately 75 to 80 percent water (for example, table 1). Low sample weights resulting from 

desiccation will bias the calculation of “wet-weight” Hg concentrations from reported dry-weight 

values. Therefore, the smallest appropriate sample container should be used, and all air expressed from 

zip-seal bags when used. Processed samples should be preserved immediately on dry ice for transport to 

a freezer or analytical laboratory and analyzed as soon as possible, preferably within 6 months. Scudder 

and others (2008) illustrate fish processing steps with detailed illustrations and close-up photographs, 

which we have not attempted to reproduce here. 

Field Data Forms

Labeling the sample properly and filling out all field forms and other paperwork correctly and 

completely are critical steps in ensuring proper data management. Blank field forms are available for 

analytical services requests and cooler inventory forms are available online from the USGS MRL. 

Examples of acceptable field data forms and sample analytical service requests follow:
23

FIELD DATA SHEET (NWIS field name noted in parentheses) 

USGS Mercury studies--Fish tissue samples Project: 

Station Name (SNAME): 

Station ID (STAID): Sample date (DATES), YYYYMMDD: 

Time range, 24h, HHMM -HHMM: Medium Code (MEDIM): C 

Sample Type (STYPE): H Analysis status (ASTAT): ME Hydrologic condition (HSTAT): A

Field Crew: 

Field comments: 

Species Common name: Latin name: 

ITIS Taxonomic code (TAXON): Body part code (BDPRT): 

Fish 

#

Sample 

time 

(TIMES)

(24 h)

Fish 

length, 

total, 

cm, 

P91106

Fish wt, 

g, 

P91104

Sample 

wt, g, 

P9110

5

Gender

, Male, 

P47463

Gender, 

Female, 

P47462

Scale/ 

Otolith Sample ID NWIS Record #

1 

2 

3 

4 

5 

6 

7 

8 

9 

10 

11 

12 

13

14

15
24

Page ___of ___ SAMPLE SUBMISSION/TRACKING FORM 

USGS Mercury studies--Fish tissue samples Shipper instructions: 

Study Unit contact: 

Phone number: 

Shipped by: 

Shipping date: 

Received by: 

Received date: 

(1) Save a COPY of this form 

(2) Enter sample data into this spreadsheet 

(3) Sign, date, and ship hard copy of completed form with samples 

(4) Email electronic copy to laboratory to facilitate lab log-in. 

Lab Instructions: 

(1) Sign, date, and note comments upon receipt of samples. 

(2) Save form. Fax or mail copy to Study Unit contact. 

Study Unit (SU) notes to lab: 

Analyses requested: Total Mercury Medium Code: C 

Lab notes / condition of samples: 

Sample data 

STAID DATES TIMES 

(24 h) Species Fish length, 

total (cm)

Fish 

wt (g)

Sampl

e Cut

Sample

wt (g)

Gender 

(M/F/I)

Sample 

ID Comments
25

Sample Shipment 

Before shipping the samples, verify that the samples have been recorded on appropriate sample 

submissions forms and call the analytical laboratory to confirm that the laboratory is prepared to 

properly receive the samples. Frozen samples must be express-shipped (next-day delivery), and must 

contain sufficient dry ice so that a 1-day delay in delivery (due to weather, for example) will not 

compromise sample integrity. Up to 2.5 kg of dry ice generally can be shipped by air express in nonairtight (vented) coolers without requiring Hazardous Material Agreements or incurring additional costs. 

Coolers with dry ice can not be airtight, require a dry ice placard, and labeling, depending on the 

shipper’s practices. Contact the shipper for specific instructions. Samples should be shipped on 

Mondays or Tuesdays to lower the risk that frozen samples will sit for days while enroute to the 

laboratory. Notify the laboratory that samples have been shipped and request a notification of receipt if 

one is not automatically provided by the laboratories. 

Paper copies of completed laboratory submission forms must accompany sample shipments. In 

addition to paper copies of laboratory submission forms, submit electronic copies to the appropriate 

laboratory to facilitate data management. Copies of all forms and record sample shipment date and, if 

available from the shipping company, the tracking number for each shipment must be retained. 

Data Review and Release

Upon receipt from the laboratory, data will be reviewed by USGS staff. Generally the data will 

be entered into the USGS National Water Information System by the laboratory, but if not, it will be the 

responsibility of USGS Idaho Water Science Center staff to do so. Data will be coded as provisional 

until quality reviewed. The review will include at least the following checks:

• Are the site identification, sample media type, species, and Integrated Taxonomic Information 

System (www.ITIS.gov) codes correct?

• Do the reported results appear reasonable based on previous data at the site or species? Is the correct 

parameter code (63792, at the time of writing) for total mercury in fish tissue used? Are data from 

field replicate samples stored under the same site and parameter code and same sample date?

• Is the relative percent difference between replicate analyses of laboratory split samples >50 percent? 

If so, the data should not be used for any purpose and should be rejected from the database.

• Is the relative percent difference between laboratory replicate samples >20 percent and <50 percent? 

If so, the data will be published, but must be flagged as not meeting quality-control objectives. 

• Was recovery of mercury or selenium from certified reference materials within ±20 percent of 

expected values?

• Can data conversions from dry weight to wet weight be reproduced? 
26

Appendix D: Cooperative Monitoring Program

This monitoring plan is intended to provide a framework for cooperative methylmercury sampling in the 

lower Boise River basin. In IDEQ’s implementation guidance, municipal dischargers are encouraged to 

establish monitoring cooperatives to help fund watershed-based statewide monitoring for 

methylmercury in fish tissue. The USEPA further recommended that the permitting authority require 

only one study per waterbody (U.S. Environmental Protection Agency, 2010). The following 

participants are current members of the cooperative monitoring program in the Boise River basin. 

City of Boise, Idaho 

City of Caldwell, Idaho (2013) 

Star Sewer and Water District, Idaho (2014) 

City of Nampa, Idaho (2017) 
Publishing support provided by the U.S. Geological Survey 

Publishing Network, Tacoma Publishing Service Center

For more information concerning the research in this report, contact the 

Director, Idaho Water Science Center

U.S. Geological Survey 

230 Collins Road

Boise, Idaho 83702

http://id.water.usgs.gov
Mebane and MacCoy— Monitoring Plan for Mercury in Fish Tissue and Water from the Boise River, Snake River, and Brownlee Reservoir, Idaho and Oregon—Open-File Report 2013–1068, ver. 1.1