Coeur d’Alene Lake, Idaho: Insights Gained from 

Limnological Studies of 1991–92 and 2004–06

Scientific Investigations Report 2008-5168

U.S. Department of the Interior

U.S. Geological Survey

Prepared in cooperation with the Coeur d’Alene Tribe 
Cover: Coeur d’Alene Lake, northern Idaho. (Photograph taken by Paul F. Woods, U.S. 

Geological Survey (retired), November 1999.)
Coeur d’Alene Lake, Idaho: Insights 

Gained From Limnological Studies of 

1991–92 and 2004–06

By Molly S. Wood and Michael A. Beckwith

Prepared in cooperation with the Coeur d’Alene Tribe

Scientific Investigations Report 2008–5168

U.S. Department of the Interior

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

DIRK KEMPTHORNE, Secretary

U.S. Geological Survey

Mark D. Myers, Director

U.S. Geological Survey, Reston, Virginia: 2008

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

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Suggested citation:

Wood, M.S., and Beckwith, M.A., 2008, Coeur d’Alene Lake, Idaho—Insights gained from limnological studies of 

1991–92 and 2004–06: U.S. Geological Survey Scientific Investigations Report 2008-5168, 40 p. 
iii

Contents

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

Introduction.....................................................................................................................................................2

Purpose and Scope ..............................................................................................................................2

Description of Study Area ...................................................................................................................3

Methods...........................................................................................................................................................5

Limnological Study, Calendar Years 1991–92 ...................................................................................5

Limnological Study, Water Years 2004–06 ........................................................................................5

Sampling Stations and Schedules .....................................................................................................6

Mass Balances of Nutrients and Trace Metals...............................................................................8

Depth Profiles and Nutrient Sample Collection.............................................................................11

Trace Metal Sample Collection ........................................................................................................11

Comparison of Limnological Conditions ..................................................................................................12

Hydrologic, Nutrient, and Trace Metal Budgets............................................................................12

Water Temperature and Water Column Transparency ................................................................15

Dissolved Oxygen Concentration and Percent Saturation ..........................................................18

Total Phosphorus ................................................................................................................................18

Dissolved Inorganic Nitrogen...........................................................................................................20

Limiting Nutrient..................................................................................................................................21

Chlorophyll-a........................................................................................................................................22

Trophic State........................................................................................................................................22

Trace Metals........................................................................................................................................23

Pelagic and Littoral Water Quality ...................................................................................................24

Physical Limnological Processes ....................................................................................................24

Hydraulic Residence Time........................................................................................................25

Wind-Generated Circulation....................................................................................................26

Routing of Inflow Plumes..........................................................................................................26

Benthic Flux .........................................................................................................................................28

Implications of Limnological Studies .......................................................................................................32

Future Monitoring and Research Needs .................................................................................................33

Summary........................................................................................................................................................33

References Cited..........................................................................................................................................35

Appendix A. Analytical Data for Samples Collected at Pelagic and Littoral Stations in 

Coeur d’Alene Lake, Calendar Years 1991–92............................................................................39

Appendix B. Analytical Data for Samples Collected at Pelagic and Littoral Stations in 

Coeur d’Alene Lake, Water Years 2004–06.................................................................................39

Appendix C. Selected Analytical Data for Quality-Control Samples Collected in 

Coeur d’Alene Lake, Water Years 2004–06.................................................................................39
iv

Figures

Figure 1. Map showing study area and locations of streamflow-gaging stations and

littoral, benthic flux, and pelagic stations, in and near Coeur d’Alene Lake,

Idaho, water years 1999 and 2004–06 ................................................... 4

Figure 2. Graph showing variation in lake stage and sampling dates at pelagic stations,

Coeur d’Alene Lake, Idaho, water years 2004–06 ....................................... 8

Figure 3. Graph showing median depths of thermocline, Secchi-disc transparency, and

euphotic zone at five pelagic stations, Coeur d’Alene Lake, Idaho, calendar

years 1991–92 and water years 2004–06 ................................................ 17

Figure 4. Graph showing minimum and maximum percent saturation of dissolved oxygen

at five pelagic stations, Coeur d’Alene Lake, Idaho, calendar years 1991–92

and water years 2004–06 .................................................................. 18

Figure 5. Graph showing median concentrations of total phosphorus in the euphotic

zone and hypolimnion at five pelagic stations, Coeur d’Alene Lake, Idaho,

calendar years 1991–92 and water years 2004–06....................................... 20

Figure 6. Graph showing median concentrations of dissolved inorganic nitrogen in the

euphotic zone and hypolimnion at five pelagic stations, Coeur d’Alene Lake,

Idaho, calendar years 1991–92 and water years 2004–06 .............................. 21

Figure 7. Graph showing median concentrations of chlorophyll-a in the euphotic zone at

five pelagic stations, Coeur d’Alene Lake, Idaho, calendar years 1991–92 and

water years 2004–06 ........................................................................ 22

Figure 8. Graph showing median concentrations of total zinc in euphotic zone and

hypolimnion at five pelagic stations, Coeur d’Alene Lake, Idaho, calendar

years 1991–92 and water years 2004–06 ................................................ 24
v

Tables

Table 1. Pelagic stations in Coeur d’Alene Lake, Idaho, common to studies in calendar

years 1991–92 and water years 2004–06 ................................................ 7

Table 2. Lake characteristics for selection of limnological sampling times at five

pelagic stations in Coeur d’Alene Lake, Idaho, water years 2004–06 ............... 7

Table 3. Littoral stations sampled in Coeur d’Alene Lake, Idaho, water years 2004–06. ...... 8

Table 4. Nutrient load budgets and errors, Coeur d’Alene Lake, Idaho, calendar years

1991–92 and water years 2004–06 ......................................................... 14

Table 5. Selected trace-metal loads and errors measured at three gaging stations near

Coeur d’Alene Lake, Idaho, calendar years 1991–92 and water years 2004–06...... 16

Table 6. Changes in method reporting limits for selected constituents sampled in Coeur

d’Alene Lake, Idaho, calendar years 1991–92 and water years 2004–06 ............ 19

Table 7. Trophic state based on lake-wide median values for three limnological

variables, Coeur d’Alene, Idaho, calendar years 1991–92 and water years

2004–06 ....................................................................................... 23

Table 8. Comparisons of medians and ranges of total phosphorus, chlorophyll-a, and

total zinc concentrations at pelagic and paired littoral stations on common

weeks sampled, Coeur d’Alene Lake, Idaho, water years 2004–05 .................. 25

Table 9. Inflow plume routing based on comparison of riverine inflow temperatures and

water column temperature ranges at pelagic station 3, Coeur d’Alene Lake,

Idaho, water years 2004–05 ............................................................... 28

Table 10. Benthic flux of dissolved metals measured by an in-situ flux chamber, Coeur

d’Alene Lake, Idaho, 1999 .................................................................. 30

Table 11. Benthic flux of nutrients and dissolved organic carbon measured by an in-situ

flux chamber, Coeur d’Alene Lake, Idaho, 1999 .......................................... 30

Table 12. Medians and ranges of concentrations of selected constituents measured in

lower hypolimnion and near sediment-water interface at pelagic station 4,

Coeur d’Alene Lake, Idaho, water years 2004-06 ....................................... 32
vi

Conversion Factors, Datums, Abbreviations, and Acronyms

Inch/Pound to SI

Multiply By To obtain

mile (mi) 1.609 kilometer (km)

square mile (mi2

) 259.0 hectare (ha)

square mile (mi2

) 2.590 square kilometer (km2) 

SI to Inch/Pound

Multiply By To obtain

centimeter (cm) 0.3937 inch (in.)

cubic hectometer (hm3

) 35,314,666.7 cubic foot (ft3)

cubic hectometer/year (hm3

/yr) 810.7 acre-foot/year (acre-ft/yr)

cubic kilometer (km3

) 0.2399 cubic mile (mi3) 

cubic meter per second (m3

/s) 70.07 acre-foot per day (acre-ft/d)

hectare (ha) 0.003861 square mile (mi2

) 

kilogram (kg) 2.205 pound avoirdupois (lb)

kilogram per day (kg/d) 2.205 pound avoirdupois per day (lb/d)

kilogram per year (kg/yr) 2.205 pound avoirdupois per year (lb/yr)

kilometer (km) 0.6214 mile (mi)

liter (L) 33.82 ounce, fluid (fl. oz)

micrograms per square centimeter 

per year (μg/cm2

/yr)

0.0000002276 ounce, avoirdupois, per square 

inch per year (oz/in2/yr)

millimeter (mm) 0.03937 inch (in.)

meter (m) 3.281 foot (ft) 

meter (m) 1.094 yard (yd) 

square meter (m2

) 10.76 square foot (ft2) 

square centimeter (cm2

) 0.1550 square inch (ft2) 

square kilometer (km2

) 247.1 acre

square kilometer (km2

) 0.3861 square mile (mi2)

Temperature in degrees Celsius (°C) may be converted to degrees Fahrenheit (°F) as follows:

°F=(1.8×°C)+32.

Altitude, as used in this report, refers to distance above the vertical datum.

Specific conductance is given in microsiemens per centimeter at 25 degrees Celsius (μS/cm at 

25°C).

Concentrations of chemical constituents in water are given either in milligrams per liter (mg/L) 

or micrograms per liter (μg/L).
vii

Conversion Factors, Datums, Abbreviations, and Acronyms—

Continued

Datums

Vertical coordinate information is referenced to the North American Vertical Datum of 1988 

(NAVD 88).

Horizontal coordinate information is referenced to the North American Datum of 1983 (NAD 83) 

unless otherwise noted.

Abbreviations and Acronyms

Abbreviations 

and Acronymn Meaning

AMLE Adjusted Maximum Likelihood Estimator

C-F chromatographic-fluorometric

CERCLA Comprehensive Environmental Response, Compensation and Liability Act

CY calendar year

DOC dissolved organic carbon

EPA U.S. Environmental Protection Agency

HPLC High-Performance Liquid Chromatography

IDEQ Idaho Department of Environmental Quality

N:P nitrogen-to-phosphorus ratios

NCSS Number Cruncher Statistical System

NRDAR Natural Resources Damage Assessment and Restoration

NWQL USGS National Water Quality Laboratory

OU3 Operable Unit 3

PAR photosynthetically active radiation

RI/FS Remedial Investigation/Feasibility Study

ROD Record of Decision

USGS U.S. Geological Survey

WY Water Year
viii

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Abstract

More than 100 years of mining and processing of metalrich ores in northern Idaho’s Coeur d’Alene River basin have 

resulted in widespread metal contamination of the basin’s 

soil, sediment, water, and biota, including Coeur d’Alene 

Lake. Previous studies reported that about 85 percent of the 

bottom of Coeur d’Alene Lake is substantially enriched in 

antimony, arsenic, cadmium, copper, lead, mercury, silver, 

and zinc. Nutrients in the lake also are a major concern 

because they can change the lake’s trophic status—or level 

of biological productivity—which could result in secondary 

releases of metals from contaminated lakebed sediments. This 

report presents insights into the limnological functioning of 

Coeur d’Alene Lake based on information gathered during two 

large-scale limnological studies conducted during calendar 

years 1991–92 and water years 2004–06.

Both limnological studies reported that longitudinal 

gradients exist from north to south for decreasing water 

column transparency, loss of dissolved oxygen, and 

increasing total phosphorus concentrations. Gradients also 

exist for total lead, total zinc, and hypolimnetic dissolved 

oxygen concentrations, ranging from high concentrations 

in the central part of the lake to lower concentrations at the 

northern and southern ends of the lake. In the southern end 

of the lake, seasonal anoxia serves as a mechanism to release 

dissolved constituents such as phosphorus, nitrogen, iron, and 

manganese from lakebed sediments and from detrital material 

within the water column.

Nonparametric statistical hypothesis tests at a 

significance level of α=0.05 were used to compare analyte 

concentrations among stations, between lake zones, and 

between study periods. The highest dissolved oxygen 

concentrations were measured in winter in association with 

minimum water temperatures, and the lowest concentrations 

were measured in the Coeur d’Alene Lake hypolimnion during 

late summer or autumn as prolonged thermal stratification 

restricted mixing of the oxygenated upper water column 

and the hypolimnion, where oxygen was consumed. Large 

differences in median concentrations of dissolved inorganic 

nitrogen were measured between the euphotic zone and 

hypolimnion in the deep areas of the lake. These differences 

in nitrogen concentrations were attributable to several 

limnological processes, including seasonal inflow plume 

routing, isolation from wind-driven circulation and associated 

hypolimnetic enrichment, phytoplanktonic assimilation during 

summer months, and benthic flux.

Increased chlorophyll-a and total phosphorus 

concentrations were measured throughout the lake in the 

2004–06 study compared with results from the 1991–92 study. 

No significant change in hypolimnetic dissolved inorganic 

nitrogen concentration throughout the lake was noted even 

though total nitrogen loads into the lake decreased between 

study periods. Total zinc and total lead decreased throughout 

the lake from the 1991-92 study to the 2004-06 study except 

in the southern part of the lake, where concentrations were 

typically low. Median detected nitrogen-to-phosphorus 

ratios decreased from the 1991–92 study to the 2004–06 

study. Whereas the lake was clearly phosphorus-limited in 

1991–92, in 2004–06 the lake may have been much closer 

to the boundary value of 7.2 that separates nitrogen from 

phosphorus limitation. However, due to changes in analytical 

reporting limits in the period between the two studies, the data 

are insufficiently certain to draw reliable conclusions with 

regard to limiting nutrients. For both studies, the trophic state 

of the lake was classified as oligotrophic (less productive) 

or mesotrophic (moderately productive), depending on the 

constituent used for classification.

Internal circulation from wind-generated waves and 

changes in the lake’s thermocline are important processes for 

distribution of water-quality constituents throughout Coeur 

d’Alene Lake. Surficial distribution of trace metals throughout 

most of the lake, including bays, is relatively uniform. Even 

south of the Coeur d’Alene River mouth, lakebed sediments 

are contaminated with trace metals. Inflow plume routing of 

the two primary inflow sources, the Coeur d’Alene and St. 

Joe Rivers, also significantly affects the fate and transport of 

contaminants. Most riverine inflows appear to move through 

the lake as overflow during summer, interflow during spring 

and autumn, and underflow during winter.

Benthic flux is another key transport process for 

contaminants in Coeur d’Alene Lake. The results of in situ 

benthic flux chamber experiments indicated movement of 

dissolved metals, nutrients, and dissolved organic carbon out 

of the lakebed sediments. However, the lake is an overall sink 

for these constituents when they are associated with particulate 

material.

Coeur d’Alene Lake, Idaho: Insights Gained From 

Limnological Studies of 1991–92 and 2004–06

By Molly S. Wood and Michael A. Beckwith
2 Coeur d’Alene Lake, Idaho: Insights Gained From Limnological Studies of 1991–92 and 2004–06

Introduction

From the late 1880s to the early 1980s, the mining 

district in the South Fork Coeur d’Alene River valley was 

among the Nation’s largest producers of silver, lead, zinc, 

and other metals. The mining and ore-processing methods 

used in the “Silver Valley” to extract this wealth produced 

large quantities of waste material containing environmentally 

hazardous contaminants such as cadmium, lead, and zinc. 

Much of this material was discharged directly to or washed 

into the South Fork Coeur d’Alene River and its tributaries. 

The beds, banks, and floodplains of the Coeur d’Alene River, 

Coeur d’Alene Lake, and to a lesser extent the Spokane River, 

contain large quantities of metal-contaminated sediments 

that are transported downstream and dispersed by hydrologic 

processes, including through Coeur d’Alene Lake, into the 

Spokane River, and into the State of Washington. Large 

quantities of metal-contaminated sediment presently reside 

in the bed of Coeur d’Alene Lake that, unless removed, will 

require long-term management actions to maintain them in 

place without risk to human health and the environment. The 

extent and magnitude of mining associated environmental 

contamination throughout the South Fork and main stem 

Coeur d’Alene River, Coeur d’Alene Lake, and Spokane River 

basins has resulted in environmental cleanup (“Superfund”) 

and Natural Resources Damage Assessment and Restoration 

(NRDAR) litigation actions under the Comprehensive 

Environmental Response, Compensation and Liability Act 

(CERCLA) that are among the largest, most complex, longest 

in duration, and costliest in the Nation. The potential for 

nutrient enrichment and subsequent eutrophication of Coeur 

d’Alene Lake also are of considerable concern because of 

land-use activities throughout the drainage basin and along 

the shoreline, as well as intensive recreational use in the lake 

(Woods and Beckwith, 1997). A nutrient load study conducted 

in 1975 as part of the National Eutrophication Survey led to 

the determination that Coeur d’Alene Lake was mesotrophic, 

or moderately productive (U.S. Environmental Protection 

Agency, 1977), which prompted continued observation of the 

lake’s trophic status.

Comprehensive studies of Coeur d’Alene Lake and the 

surrounding watershed were conducted in the late 1980s 

and early 1990s by the U.S. Geological Survey (USGS) and 

Coeur d’Alene Tribe in cooperation with Idaho Department of 

Environmental Quality (IDEQ) (Woods, 1989; Horowitz and 

others, 1993, 1995a, 1995b; Woods and Berenbrock, 1994; 

Woods and Beckwith, 1997).

In 1998, the U.S. Environmental Protection Agency 

(USEPA) began a Remedial Investigation/Feasibility Study 

(RI/FS) to assess mining associated contamination outside 

the original 21 mi2

 Bunker Hill Mining and Metallurgical 

Complex Superfund Site surrounding the communities of 

Kellogg and Smelterville, Idaho. USGS researchers were 

involved in the RI/FS by establishing and operating the Coeur 

d’Alene Basin Environmental Monitoring Program to monitor 

hydrological conditions and constituent concentrations and 

transport throughout the Coeur d’Alene River basin, and by 

conducting additional, highly focused limnological sampling 

of contaminant transport through the lake and geochemical 

research of contaminant flux at the sediment-water interface. 

In 2000, the U.S. 9th Circuit Court of Appeals ruled that the 

Bunker Hill Site includes all areas in the Coeur d’Alene Lake/

Spokane River basin (the Basin) where hazardous substances 

have come to be located. In 2002, the USEPA issued a 

Record of Decision (ROD) (U.S. Environmental Protection 

Agency, 2002) for Operable Unit 3 (OU3) of the Bunker 

Hill Superfund Site describing about 30 years of prioritized 

remedial actions for cleanup throughout the basin.

The selected remedy for OU3 did not include actions for 

Coeur d’Alene Lake. This decision was deferred pending the 

development and effective implementation of a revised Lake 

Management Plan to protect water quality and to effectively 

contain and prevent mobilization of metals from lakebed 

sediments. A draft Lake Management Plan was developed 

in June 2008 (IDEQ and Coeur d’Alene Tribe, 2008). When 

finalized, it will be implemented by State, tribal, Federal, and 

local governments outside of the formal CERCLA process 

using separate regulatory authorities and funding.

Purpose and Scope

This report presents insights into the limnological 

functioning of Coeur d’Alene Lake based on information 

developed from two large-scale limnological studies of the 

lake conducted by the USGS and the Coeur d’Alene Tribe 

during calendar years 1991–92 and water years 2004–06. 

The data collection and evaluation activities of the 2004–06 

limnological studies discussed in this report were designed to 

provide information for the Bunker Hill Superfund Site OU3 

and the Lake Management Plan (specified in the OU3 ROD to 

be developed and implemented instead of a formal CERCLA 

remedy).

The 2004–06 study included sampling and evaluation 

of limnological characteristics not covered by the 1991–92 

study. An important goal of the 2004–06 study was to 

better understand the interaction of physical, chemical, and 

biological processes in the lake to aid in the interpretation of 

future water-quality trends in Coeur d’Alene Lake as remedial 

actions are undertaken under the OU3 ROD and the Lake 

Management Plan. The study design sought to evaluate the 

interaction of trace metals, nutrients, and lake productivity 

during water years 2004–06 using highly focused sampling of 
Introduction 3

physical, chemical, and biological characteristics over a range 

of spatial and temporal conditions. The study’s technical scope 

covered the following data collection and evaluation activities: 

(1) mass balances of trace metals and nutrients, (2) fate and 

transport of nutrients and quantification of lake productivity, 

and (3) fate and transport of trace metals.

In this report, important limnological characteristics 

measured by both studies are compared to gain understanding 

of the complex interaction of physical, chemical, and 

biological processes in the lake and the resulting water-quality 

conditions, to assess temporal and spatial differences, and to 

identify potential changes and trends in lake water quality over 

time. The insights gained from the two studies can be used 

in the decision-making process for managing Coeur d’Alene 

Lake water quality and contaminants in the basin.

Description of Study Area

Coeur d’Alene Lake—Idaho’s second largest lake—is in 

northern Idaho (fig. 1) in the 17,300-km2 Spokane River basin. 

The lake was created about 18,000–13,000 years ago, after a 

series of outburst floods from glacial Lake Missoula deposited 

about 100 m of coarse gravel deposits in the Rathdrum PrairieSpokane River Valley, damming the Pleistocene Spokane 

River and its two primary tributaries, the Coeur d’Alene 

and St. Joe Rivers (URS Greiner, Inc., and CH2M Hill, Inc., 

2001). Present-day Coeur d’Alene Lake covers 129 km2 at full 

summer pool elevation of 649.8 m (NAVD 88) and is about 

35-km long in a north-south orientation. The maximum width 

is about 3.7 km, and the maximum depth is about 64 m. The 

volume is 2.8 km3 at full pool (Woods and Berenbrock, 1994).

The southern end of the lake, under Tribal jurisdiction, 

is contiguous with four shallow lakes (Benewah, Chatcolet, 

Hidden, and Round Lakes) that were primarily emergent 

wetlands prior to the 1906 construction of Post Falls Dam 

on the Spokane River downstream of the lake outlet. Dam 

operation provides storage for hydroelectric power generation 

by maintaining the lake surface elevation approximately 

2.1-m higher than normal, following spring runoff, through 

late summer as the lake recedes. By delaying lake recession 

until late summer or early autumn, dam operation has created 

large expanses of shallow open water areas, increased habitat 

for aquatic macrophyte growth, and altered the natural levees, 

lateral lakes, and wetlands ecosystems in the lower reaches of 

the Coeur d’Alene and St. Joe Rivers.

The drainage area of Coeur d’Alene Lake is about 

9,690 km2; most (90 percent) of the lake’s inflow is 

delivered by the Coeur d’Alene and St. Joe Rivers (Woods 

and Beckwith, 1997). Coeur d’Alene Lake outflows to 

the Spokane River, a tributary of the Columbia River. The 

drainage area of the lake is comprised mostly of mountains 

covered in coniferous forests and deep, intermontane valleys. 

The Coeur d’Alene and St. Joe Rivers originate in the Coeur 

d’Alene and St. Joe Mountains, respectively, which are 

sub-ranges of the Bitterroot Mountains that form the IdahoMontana border. Elevations range from about 650 m (NAVD 

88) near the lake outlet to about 2,090 m (NAVD 88). About 

78 percent of the land cover in the drainage area is forest 

(coniferous, sparse, or recovering harvest), and rangeland and 

agriculture account for about 7 and 5 percent, respectively. 

The remaining 10 percent of the land cover, in order of largest 

to smallest area, is clear cut/barren land, small water bodies, 

wetlands, and urban and mine areas.

Annual precipitation in the drainage basin is higher 

than other areas in Idaho. Snowfall between October and 

April comprises about 70 percent of the annual precipitation. 

The influence of Pacific Maritime conditions can produce 

large rain-on-snow events during winter. The mountainous 

topography of the basin affects the spatial distribution of 

precipitation. For example, mean annual precipitation is about 

64 cm at the lake, whereas mean annual precipitation is about 

97 cm at Wallace, Idaho, a town in the drainage basin, which 

is about 75 km east and 250-m higher in elevation than the 

lake. Ambient temperature varies similarly, and although 

winter temperatures at Coeur d’Alene Lake often are below 

freezing, the lake does not typically freeze except at the 

shallow southern end.

The Coeur d’Alene River (drainage area 3,810 km2

) 

discharges into the southern one-third of the lake near 

Harrison, Idaho, and is comprised of three major reaches: 

the North Fork, the South Fork, and below the confluence of 

the North and South Forks (not shown in figures). Primary 

land-use activities in the North Fork drainage basin include 

recreation, forestry, and agriculture, with limited historical 

placer and hard-rock mining. Extensive hard-rock mining, 

ore processing, and transportation activities occurred in the 

South Fork Coeur d’Alene River drainage basin. Known as the 

“Silver Valley”, the South Fork basin was among the Nation’s 

largest producers of silver, lead, and zinc for almost a century; 

currently, it includes one of the Nation’s largest Superfund 

sites with only limited mining and ore processing. The St. 

Joe River (drainage area 4,520 km2

) discharges into the 

extreme southern end of the lake, several miles downstream 

of the confluence of the St. Joe and St. Maries Rivers near 

St. Maries, Idaho. Recreation, forestry, and agriculture are 

the dominant land uses in the St. Joe River drainage area, and 

little mining activity has occurred. Urban land use is relatively 

low (less than 1 percent as of 1997) in the St. Joe and St. 

Maries River basins (Woods and Beckwith, 1997). However, 

considerable population growth and land development is 

occurring near the lake, including several proposed golf resort 

communities and marinas.
4 Coeur d’Alene Lake, Idaho: Insights Gained From Limnological Studies of 1991–92 and 2004–06

id19-0064_fig01

0 5

5

10 15 MILES

0 10 15 KILOMETERS

Base from U.S. Geological Survey digital data. 1:24,000 quadrangles, 1981

Universal Transverse Mercator (UTM) projection, Zone 11

Coeur d’Alene

Post Falls

St. Maries

to Plummer

Harrison

Littoral station, 

 south 2004–06 study

Littoral station, north 2004–06 study 

Benthic flux station

Streamflow-gaging station

12413860 Coeur d'Alene River near Harrison

12415075 St. Joe River at St. Maries

12415140 St. Joe River near Chatcolet

12417598 Spokane River at Lake Outlet at 

 Coeur d'Alene

12419000 Spokane River near Post Falls

NS1 Shingle Bay

BF1 Main Channel

BF2 Mica Bay

NS2 Mouth Coeur d’Alene River

NS3 Windy Bay

NS4 Rockford Bay

NS5 Powderhorn Bay

NS6 Carlin Bay

NS7 Loffs Bay

NS8 Mica Bay

NS9 Echo Bay

NS10 Kid Island Bay

NS11 Cougar Bay

NS12 Beauty Bay

Pelagic station

1 Tubbs Hill

3 Driftwood Point

4 University Point

5 Blue Point

6 Chatcolet Lake

S1 Carey Bay

S2 O’Gara Bay

S3 Cal’s Pond Area

S4 Dean’s Wetland Area

S5 East Causeway Bend

S6 East Causeway

EXPLANATION WASHINGTON IDAHO

Coeur d’Alene Lake

Fighting Creek

Plummer Creek

Coeur d’Alene

River Harrison

slough

Anderson

Lake

Chatcolet Lake

Hidden Lake

Round Lake

Benewah Lake

Black

Lake

Thompson

Lake

Blue

Lake

Swan

Lake

Medicine

Lake

Killarney

Lake

Cave

Lake

Wolf Lodge Creek

Carlin

 Creek

Windy

Bay

Rockford

Bay

Mica

Bay

Cougar

Bay

Wolf

Lodge

Bay

Carlin

Bay

Powderhorn

Bay

 

St. Joe River

St. Maries 

River

SPOKANE

RIVER

WASHINGTON

Study area

IDAHO

I

90

I

90

US

95

US

95

SR

3

SR

3

SR

97

SR

5

SR

3

SR

97

6

5

4

3

1

S1 S2

S3

S5

S4

S6

NS2

NS3

NS4

NS1

NS5

NS6

NS7

NS8

NS9

NS10

NS11

NS12

12415140

12415075

12413860

12419000

12417598

BF1

BF2

BENEWAH CO.

KOOTENAI CO.

Coeur d’Alene Indian Reservation

Coeur d’Alene Indian Reservation

to Bunker Hill 

Superfund site

Coeur d'Alene Mountains

St. Joe Mountains

117°00’ 116°45’ 47°45’

47°30’

47°15’

116°30’

Figure 1. Study area and locations of streamflow-gaging stations and littoral, benthic flux, and pelagic 

stations, in and near Coeur d’Alene Lake, Idaho, water years 1999 and 2004–06.
Methods 5

Methods

Limnological Study, Calendar Years 1991–92

The 1991–92 study was conducted during 2 calendar 

years, beginning in mid-January 1991 and ending in midDecember 1992. Seven pelagic stations were sampled every 

3 weeks from May through October and every 4 to 6 weeks 

during the remaining months. Pelagic stations were located 

in the open water, deeper (10 m or more) areas of the lake. A 

full description of the sampling design and rationale for the 

1991–92 study is provided in Woods and Beckwith (1997).

Full-depth profiles of water column temperature, specific 

conductance, pH, and dissolved oxygen concentration 

and percent saturation were measured. Secchi-disc 

transparency depth was measured and the euphotic zone 

depth was determined based on water column profiles of 

photosynthetically active radiation (PAR) intensity. Within the 

euphotic zone, a composite sample was derived from three 

point samples that were collected with a non-metallic Van 

Dorn bottle. Two additional point samples were collected at 

mid-depth and 1 m above the lakebed. These water samples 

were analyzed for concentrations of total phosphorus, 

dissolved orthophosphate, total organic plus ammonia 

nitrogen, dissolved ammonia, and dissolved nitrite plus 

nitrate. Chlorophyll-a was determined for the euphotic zone 

composite samples. On alternating sampling trips, euphotic 

zone and near-bottom samples were analyzed for total 

recoverable concentrations of arsenic, cadmium, copper, lead, 

mercury, and zinc. The water samples were analyzed at the 

USGS National Water Quality Laboratory (NWQL).

Comparisons of pelagic (open water) and littoral zone 

(near shore) water quality were made on two occasions and 

were based on 2-m-deep littoral zone samples and euphotic 

zone composite samples from the pelagic stations. During 

September 1991, 20 littoral and 6 pelagic stations were 

sampled concurrently for nutrients, chlorophyll-a, and 

dissolved oxygen. During August 1992, 15 littoral and 6 

pelagic stations were sampled concurrently for those same 

variables plus total zinc. Littoral zone sampling on both 

occasions covered stations throughout the lake (Woods and 

Beckwith, 1997).

No records could be located for quality assurance/quality 

control samples collected during the 1991-92 study. Therefore, 

no assessment could be made to determine if equipment 

decontamination procedures were adequate to remove analytes 

of interest or to quantify variability introduced during sample 

processing and analysis.

Limnological Study, Water Years 2004–06

Samples were collected by USGS crews at five stations in 

the pelagic zone (fig. 1; also sampled during 1991–92), eight 

times each year during water years 2004–06. A water year 

is from October 1 through September 30. As in the 1991–92 

limnological study, full-depth profiles of the water column 

temperature, specific conductance, pH, and dissolved oxygen 

concentration and percent saturation were measured. Secchidisc transparency depth was measured, and the euphotic 

zone depth was determined with water column profiles of 

PAR intensity. Within the euphotic zone, a composite sample 

was collected using a pump sampler lowered through the 

euphotic zone. Additional point samples were collected at 

depths representing the upper hypolimnion and 1 m above the 

lakebed representing the lower hypolimnion. Water samples 

were analyzed at the USGS NWQL.

Coeur d’Alene Tribe crews collected samples at 12 

stations in the littoral zone on 4 occasions in water year 2004 

and at 18 stations on 4 occasions in water year 2005 and 

early in 2006. These sites were primarily near the heads of 

bays, in water about 4-m deep, and generally within 20 m of 

the lakeshore (fig. 1). Point samples were collected from a 

depth of 2 m, where temperature, specific conductance, pH, 

and dissolved oxygen concentration and percent saturation 

also were measured. Coeur d’Alene Tribe crews sampled 

the littoral stations during the same week that USGS crews 

sampled the pelagic stations. Littoral zone samples were 

shipped by USGS to the NWQL for analyses.

Comparisons of pelagic and littoral zone water quality 

were made on two occasions and were based on 2-m-deep 

littoral zone samples and euphotic zone composite samples 

from the pelagic stations. During August 2004, 12 littoral and 

5 pelagic stations were sampled concurrently for nutrients, 

chlorophyll-a, and metals. During July 2005, 18 littoral and 

5 pelagic stations were sampled concurrently for the same 

variables.

Quality assurance/quality control samples were collected 

during routine sampling trips. Field blank samples were 

submitted to the NWQL at a frequency of 4 percent to assess 

whether equipment decontamination procedures were adequate 

to remove analytes of interest. Three source solution blanks 

were submitted to assess possible contamination in blank 

water used in the field blank samples. Duplicate or replicate 

samples were submitted at a frequency of 5 percent to assess 

variability introduced during sample processing and analysis.

The 2004–06 study approach was designed to 

complement previous limnological studies of the lake that 

were done mostly by the USGS since 1987 (Woods, 1989; 

Horowitz and others, 1993, 1995a, 1995b; Woods and 

Berenbrock, 1994; Woods and Beckwith, 1997; Balistrieri, 

1998; Kuwabara and others, 2000; Woods, 2004). The study 

approach also incorporated important new limnological 

information obtained from the RI/FS of the lake conducted by 

the USGS for USEPA during 1999 in support of the Bunker 

Hill Superfund Site OU3 ROD (URS Greiner, Inc., and CH2M 

Hill, Inc., 2001; CH2M Hill, Inc., and URS Corp., 2001).

The RI/FS (URS Greiner, Inc., and CH2M Hill, Inc., 

2001) and a USGS evaluation (funded by the National Water 

Quality Assessment Program) of fate and transport processes 
6 Coeur d’Alene Lake, Idaho: Insights Gained From Limnological Studies of 1991–92 and 2004–06

in Coeur d’Alene and Pend Oreille Lakes in northern Idaho 

and Flathead Lake in northwestern Montana (Woods, 2004) 

reported that lake hydrodynamics and riverine inflow plume 

routing played important roles in the fate and transport of 

constituents and, by extension, water-quality conditions in 

the lakes. Therefore, limnological data collection in Coeur 

d’Alene Lake during water years 2004–06 was scheduled 

during important periods related to lake hydrodynamics and 

limnological conditions.

The approaches used for the two studies were similar in 

many respects and allowed for robust comparisons between 

most analytes. Two differences in approach merit further 

discussion: (1) compositing of euphotic zone samples, and 

(2) analytical methods for determination of chlorophyll-a

concentrations.

Water-quality profiling instrumentation used in the 

2004–06 study provided high resolution (less than 0.1 

m) data that revealed substantial variations in constituent 

concentrations within the euphotic zone, especially during 

periods of thermal stratification. This variability was 

represented in the pumped-sample compositing used in 

the 2004–06 study. The 3-point sample compositing used 

in the 1991–92 study was less likely to have obtained a 

representative sample of the euphotic zone.

Concentrations of chlorophyll-a for the 1991–92 

study were determined with High-Performance Liquid 

Chromatography (HPLC) using methods from Britton and 

Greeson (1989). Prior to the start of the 2004–06 study, 

however, the USGS NWQL replaced the HPLC method with a 

chromatographic-fluorometric (C-F) method, presented in U.S. 

Geological Survey National Water Quality Laboratory (2000) 

and Britton and Greeson (1989). Reasons for the change in 

analytical methods were provided by U.S. Geological Survey, 

National Water Quality Laboratory, written commun., 2005. 

This change presented potential difficulties in comparing 

concentrations of chlorophyll-a between the two studies. 

The approach presented in this report to quantify differences 

between the two methods relied on the results of a NWQL 

comparability study where results of the two methods could 

be correlated through a regression equation (R. Brenton 

and P. Soliven, U.S. Geological Survey, written commun., 

October 1995). The regression equation reported in the 

NWQL study was derived from 39 paired samples and had the 

following form, with a coefficient of determination of 0.771:

(C–F) = 0.45801 + 0.92047 (HPLC), (1)

where:

C–F is chlorophyll-a concentration, in micrograms per 

liter, determined with the C-F method, and

HPLC is chlorophyll-a concentration, in micrograms per 

liter, determined with the HPLC method.

Equation 1 indicated that C-F values of 1.4, 5.1, and 18, 

respectively, were associated with HPLC values of 1.0, 5.0, 

and 19.

In conjunction with the work described in this report, 

a lake process simulation model called ELCOM-CAEDYM 

was developed for Coeur d’Alene Lake by the Centre for 

Water Research of the University of Western Australia under a 

cooperative agreement with the USGS and IDEQ. The goal of 

the model development was to provide agencies involved with 

the lake management decision process with a sophisticated 

tool to simulate lake response to a wide range of mining 

associated contaminant remediation and nutrient management 

strategies likely to occur or be proposed under the Bunker 

Hill Superfund Site OU3 ROD and Lake Management Plan. 

A detailed description of the model that was adapted to Coeur 

d’Alene Lake is available at http://www.cwr.uwa.edu.au 

(Hipsey and others, 2006). The USGS limnological studies 

of 1991–92 and 2004–06 were primary data sources for the 

application of the model to Coeur d’Alene Lake.

Sampling Stations and Schedules

Pelagic zone sampling was conducted at five stations 

common to the 1991–92 and 2004–06 studies (fig. 1; table 1). 

Stations are identified by number as 1, 3, 4, 5, and 6. These 

stations have been sampled historically by USGS (Woods 

and Beckwith, 1997), IDEQ (G.F. Harvey, Idaho Department 

of Environmental Quality, written commun., 2000), and the 

USEPA during the RI/FS (URS Greiner, Inc., and CH2M 

Hill, Inc., 2001). Representative lake volumes were assigned 

to each pelagic station by digitizing a bathymetric map of 

the lake, developing area polygons by joining midpoints of 

lines drawn between stations, and calculating lake volume 

under each polygon footprint. According to this method, the 

total lake volume represented by each station is: station 1, 

27 percent; station 3, 34 percent; station 4, 34 percent; station 

5, 4 percent; and station 6, 1 percent. Although stations 5 and 

6 together represent only 5 percent of the lake volume, they 

are important because they characterize the southern end of 

the lake, which is more productive than other parts of the lake. 

Water quality in this area is determined mostly by the St. Joe 

River inflow. Station 6 provides a reference condition for 

metals concentrations, which when detected, typically are low.

Limnological samples were collected at the five 

pelagic stations eight times each year during water years 

2004–06. Timing of sample collection reflects temporal 

patterns associated with lake hydrodynamics, nutrients, 

lake productivity, and fate and transport of trace metals and 

nutrients (table 2). Dates of sample collection at pelagic 

station 4 (representative of the other four stations) and lake 

stage during water years 2004–06 are shown in figure 2.
Methods 7

Station

No. Station location Latitude, longitude Depth (m)

1 1.3 mi southeast of Tubbs Hill, near Coeur d’Alene 47°39'00", 116°45'30" 42.5

3 0.8 mi southwest of Driftwood Point, near Coeur d’Alene 47°35'00", 116°48'20" 52.0

4 1.7 mi northeast of University Point, near Harrison 47°30'54", 116°50'06" 40.0

5 Northeast of Blue Point, near Harrison 47°25'00", 116°45'00" 16.5

6 Chatcolet Lake, 0.4 mi northwest of Rocky Point, near Plummer 47°21'20", 116°45'10" 11.0

Table 1. Pelagic stations in Coeur d’Alene Lake, Idaho, common to studies in calendar years 1991–92 and 

water years 2004–06.

[Station locations are shown in figure 1. Latitude, longitude in degrees, minutes, seconds, North American Datum of 1983. Depth: Lake 

surface at full-pool elevation of 649.8 meters (North American Vertical Datum of 1988). Abbreviations: m, meter; mi, mile]

Month Sample collection Lake characteristics

October 

(mid-month)

Yes Weakening stratification, drawdown cycle, decreased productivity, maximum dissolved oxygen 

depletion, increased hypolimnion storage of trace elements.

November 

(late month)

Yes Water-column circulation, stable pool, low productivity, dissolved oxygen replenishment, 

circulation of nutrients and trace elements.

December No Similar to November, but cooler temperatures.

January 

(late month)

Yes Inverse stratification, stable pool, low productivity, dissolved oxygen replenishment, circulation 

of nutrients and trace elements, follows several months of zinc-rich inflows from Coeur 

d’Alene River.

February No Similar to January, but rain-on-snow events may have raised elevation and input nutrients and 

trace elements.

March No Similar to February.

April 

(mid-month)

Yes Pre-snowmelt runoff conditions, assess distribution of dissolved oxygen, nutrients, and trace 

elements at end of winter conditions.

May 

(peak of runoff)

Yes Fill cycle from snowmelt runoff, early stratification, increased productivity if not too turbid, 

assess distribution of dissolved oxygen, nutrients, and trace elements as affected by snowmelt 

runoff and water-column circulation.

June 

(mid-month)

Yes Thermally stratified, stable summer pool, increasing productivity, start of dissolved oxygen 

depletion, increased stratification of nutrients and trace elements.

July 

(mid-month)

Yes Similar to June, but stronger stratification and dissolved oxygen depletion.

August 

(mid-month)

Yes Similar to July.

September No Similar to August but start of drawdown cycle.

Table 2. Lake characteristics for selection of limnological sampling times at five pelagic stations in Coeur d’Alene Lake, Idaho, 

water years 2004–06.

[Lake characteristics: Related to hydrodynamics, nutrients and productivity, fate and transport of trace elements]

Littoral zone sampling locations were not identical for the 

1991–92 and 2004–06 studies. Two sets of stations were used 

for sampling during 2004–06. During water years 2004–06, 12 

stations representative of bays throughout the lake (identified 

as “NS”) were sampled 4 times each year. In water year 2005, 

6 additional stations were sampled in the southern end of 

the lake near seeps (identified as “S”) to assess trace-metal 

contamination adjacent to a former mining industry railroad 

upstream of the lake. Station locations and sample dates 

for the 18 littoral stations are listed in table 3 and shown in 

figure 1. Most littoral zone samples were collected at the 2-m 

depth in water columns that were about 4-m deep and within 

about 20 m of the shoreline.
8 Coeur d’Alene Lake, Idaho: Insights Gained From Limnological Studies of 1991–92 and 2004–06

Mass Balances of Nutrients and Trace Metals

The evaluation of nutrient and trace metal mass 

balance in this report was based on annual values derived 

from constituent load information generated for five USGS 

streamflow-gaging stations in Idaho: Coeur d’Alene River 

near Harrison (12413860); St. Joe River at St. Maries 

(12415075); St. Joe River near Chatcolet (12415140); 

Spokane River at Lake Outlet at Coeur d’Alene (12417598); 

and Spokane River near Post Falls (12419000) (fig. 1). 

Periodic hydrograph-based monitoring at the five gaging 

stations provided streamflow and concentration data required 

for load calculations. The 1991–92 study reported annually 

based hydrologic, nutrient, and trace metal budgets for Coeur 

d’Alene Lake (Woods and Beckwith, 1997). Three major 

differences between the 1991–92 and 2004–06 studies were: 

(1) additional constituents were measured in the 1991–92 

study, and some common constituents had different method 

reporting limits in the 2004-06 study, (2) loads for the 

1991–92 study published in Woods and Beckwith (1997) 

were calculated using the computer program FLUX (Walker, 

1996) and loads for the 2004–06 study were calculated 

Station 

No. Station name Latitude, longitude Sampling schedule

Littoral station, north

NS1 Shingle Bay 47°24'48", 116°44'25" October, April, June, and August of water year 2004; December, 

NS2 Mouth Coeur d’Alene River 47°27'21", 116°47'30" May, and July of water year 2005; October of water year 2006.

NS3 Windy Bay 47°27'50", 116°55'59"

NS4 Rockford Bay 47°30'18", 116°54'02"

NS5 Powderhorn Bay 47°29'44", 116°49'15"

NS6 Carlin Bay 47°32'12", 116°46'40"

NS7 Loffs Bay 47°32'26", 116°49'32"

NS8 Mica Bay 47°35'54", 116°51'11"

NS9 Echo Bay 47°36'27", 116°46'08"

NS10 Kid Island Bay 47°38'45", 116°48'00"

NS11 Cougar Bay 47°40'23", 116°48'44"

NS12 Beauty Bay 47°36'53", 116°41'17"

Littoral station, south

S1 Carey Bay 47°24'40", 116°46'08" December, May, and July of water year 2005; October of water 

S2 O’Gara Bay 47°24'08", 116°44'23" year 2006.

S3 Cal’s Pond Area 47°23'37", 116°44'40"

S4 Dean’s Wetland Area 47°23'04", 116°44'18"

S5 East Causeway Bend 47°22'50", 116°44'23"

S6 East Causeway 47°22'44", 116°44'33"

Table 3. Littoral stations sampled in Coeur d’Alene Lake, Idaho, water years 2004–06.

[Station locations are shown in figure 1. Station No.: NS, nearshore; S, seep. Latitude, longitude: degrees, minutes, seconds, North American Datum of 1983]

02

647

648

649

650

651

LAKE STAGE, IN METERS ABOVE NAVD 88

Normal full-pool elevation = 649.8 meters

Sept. 25

Nov. 25

Jan. 25

Mar. 25

May 25

July 25

Sept. 25

Nov. 25

Jan. 25

Mar. 25

May 25

July 25

Sept. 25

Nov. 25

Jan. 25

Mar. 25

May 25

July 25

Sept. 25

2003 2004 2005 2006

Lake stage

Pelagic sampling

Figure 2. Variation in lake stage and sampling dates at 

pelagic stations, Coeur d’Alene Lake, Idaho, water years 

2004–06.
Methods 9

using the computer program LOADEST (Runkel and others, 

2004), and (3) sampling locations changed on the St. Joe and 

Spokane Rivers between studies. For this report, only loads 

measured in common between the two studies were compared. 

The accuracy of the load budgets is affected by changes in 

method reporting limits after the NWQL updated analytical 

procedures in the late 1990s, and a robust direct comparison 

cannot be made for all constituents. The 1991–92 loads were 

recalculated using LOADEST so a proper comparison could 

be made with the 2004–06 loads. The LOADEST program 

uses a multiple linear regression approach to calculate 

loads based on available streamflow records, decimal time, 

seasonality functions, and other user-input explanatory 

variables (Runkel and others, 2004). The Adjusted Maximum 

Likelihood Estimator (AMLE) regression model in the 

LOADEST program was used to incorporate censored data 

with multiple reporting limits.

The gaging station on the St. Joe River was moved from 

St. Maries (12415075) to Chatcolet (12415140) between the 

1991–92 and 2004–06 studies to capture total inflow to the 

lake from the St. Joe River. The station sampled during the 

1991–92 study, 12415075, did not capture nutrient inputs 

from the St. Maries wastewater treatment plant because it was 

upstream of the plant outfall. Similarly, the gaging station on 

the Spokane River was moved from Post Falls (12419000) 

to Coeur d’Alene (12417598) between the 1991–92 and 

2004–06 studies to quantify water-quality conditions at the 

primary outlet of the lake. Water-quality conditions at the 

station sampled in 1991–92, 12419000, were influenced by 

nutrients in effluent from the Coeur d’Alene, Hayden, and 

Post Falls municipal wastewater treatment plants. The gaging 

station sampled in 2004–06, 12417598, was upstream of these 

plant outfalls. The location of the gaging station on the Coeur 

d’Alene River, 12413860, remained constant between the 

study periods.

Nutrient load data for the Spokane and St. Joe Rivers 

in the 1991–92 study period were normalized to locations 

sampled during the 2004–06 study period for comparison 

of loads. Nutrient loads contributed by wastewater effluent 

were subtracted from the 1991–92 loads measured at station 

12419000, Spokane River near Post Falls, to obtain a measure 

of nutrient loads at the lake outlet. Similarly, nutrient loads 

from wastewater effluent were added to the 1991–92 loads 

measured at station 12415075, St. Joe River at St. Maries. 

Trace metal loads were not normalized for sampling location 

because no data were available for computing additional 

inputs or losses, if any, between the sampling locations on 

the Spokane and St. Joe Rivers. Additional inputs or losses 

between sampling locations for trace metal loads are assumed 

to be negligible.

Total nitrogen and total phosphorus loads in effluent 

from the St. Maries wastewater treatment plant to the St. Joe 

River in 1991–92 were reported as 3,720 kg/yr and 1,400 kg/

yr, respectively, in Woods and Beckwith (1997). Average 

monthly loads for total phosphorus in wastewater effluent 

to the Spokane River were calculated from records provided 

by the Coeur d’Alene and Hayden municipal wastewater 

treatment plants. Average monthly loads for total nitrogen 

effluent were calculated for the Coeur d’Alene plant. Nitrogen 

compounds were not monitored in effluent from the Hayden 

plant during 1991–92; therefore, records were not available for 

calculation of nitrogen loads. Nutrient inputs from the Hayden 

plant were small compared to nutrient inputs from the Coeur 

d’Alene plant, and wastewater effluent was discharged to a 

land application site, not directly to the Spokane River, for 

most months in 1991–92. Consistent monitoring records were 

not available for the Post Falls wastewater treatment plant in 

1991–92, but the plant discharged to the Spokane River yearround during the 1991–92 study period (Mark Barkley, City 

of Post Falls, oral commun., July 2008). Therefore, nutrient 

loads from the Post Falls treatment plant were estimated by 

multiplying nutrient loads from Coeur d’Alene treatment 

plant effluent by a ratio between the populations of Coeur 

d’Alene and Post Falls in 1991–92, according to the following 

equation:

PF WWTP nutrient load

 = CdA WWTP nutrient load

 × (PF population/CdA population), (2)

where

PF WWTP nutrient load is the estimated total monthly 

nutrient (nitrogen or 

phosphorus) load in Post Falls 

wastewater treatment plant 

effluent, in kilograms;

CdA WWTP load is the measured total monthly 

nutrient (nitrogen or 

phosphorus) load in 

Coeur d’Alene wastewater 

treatment plant effluent, in 

kilograms; and

PF and CdA populations are the population estimates for 

the cities of Post Falls and 

Coeur d’Alene, respectively, 

for 1991 and 1992, according 

to the U.S. Census Bureau 

(2000), in number of people.
10 Coeur d’Alene Lake, Idaho: Insights Gained From Limnological Studies of 1991–92 and 2004–06

Annual loads of nutrients from ungaged surface-water 

inflows, including Plummer, Fighting, Carlin, and Wolf Lodge 

Creeks, were measured during the 1991–92 study and reported 

in Woods and Beckwith (1997). Ungaged surface-water 

inflows were not sampled during the 2004–06 study; however, 

nutrient concentrations in inflows from these ungaged inflows 

were assumed to be relatively constant between the 1991–92 

studies because nutrient sources in these tributaries primarily 

are agricultural and natural sources, not municipal wastewater 

treatment plant effluent. Nutrient loads in ungaged surfacewater inflows in the 2004–06 study were estimated for 

Plummer, Fighting, Carlin, and Wolf Lodge Creeks as well 

as for other ungaged surface water including small tributaries 

and runoff. Nutrient coefficients were calculated by relating 

the measured 1991 and 1992 nutrient load in a particular creek 

to the measured flow volume in the nearest gaged inflow, the 

Coeur d’Alene or St. Joe Rivers, for the same year. The 1991 

and 1992 nutrient coefficients then were averaged. Inputs from 

“other” ungaged surface water inflows were related to the 

combined flow of the Coeur d’Alene and St. Joe Rivers as the 

exact locations of these sources are unknown. The equation 

for the average nutrient coefficient for ungaged surface-water 

inflows had the following form:

Cavg = ((L91/Qnear91) + (L92/Qnear92))/2, (3)

where:

Cavg is the average nutrient (nitrogen or phosphorus) 

coefficient for a given ungaged surface water 

inflow, in kilograms per cubic hectometer;

L91 is the total nutrient (nitrogen or phosphorus) load 

for a given ungaged surface water inflow in the 

1991 study, in kilograms;

Qnear91 is the total flow volume of the gaged surface-water 

inflow, the Coeur d’Alene or St. Joe River, 

closest to the ungaged surface-water inflow in the 

1991 study, in cubic hectometers;

L92 is the total nutrient (nitrogen or phosphorus) load 

for a given ungaged surface water inflow in the 

1992 study, in kilograms; and

Qnear92 is the total flow volume of the closest gaged 

surface-water inflow in the 1992 study, in cubic 

hectometers.

The average nutrient coefficient from the 1991–92 study 

was then used to estimate loads from ungaged surface-water 

inflows for each year during the 2004–06 study according to 

the following equation:

L = Cavg x Qnear, (4)

where:

L is the estimated total annual nutrient (nitrogen or 

phosphorus) load for a given ungaged surface water 

inflow for a given year in the 2004–06 study, in 

kilograms;

Cavg is the average nutrient coefficient for a given ungaged 

surface water inflow, in kilograms per cubic 

hectometer; and

Qnear is the total flow volume of the gaged surface-water 

inflow, the Coeur d’Alene or St. Joe River, closest 

to the ungaged surface-water inflow for a given 

year in the 2004–06 study, in cubic hectometers.

Annual nutrient loads from precipitation and other 

atmospheric sources in the 1991–92 study were estimated 

and published in Woods and Beckwith (1997) based on data 

presented by Stanford and others (1983), Hallock and Falter 

(1987) and National Atmospheric Deposition Program (1991). 

These values were assumed to be constant for the 2004–06 

study. Annual nutrient loads from private and community 

wastewater-treatment systems in the nearshore area of the lake 

were estimated for the 1991–92 study and published in Woods 

and Beckwith (1997). These values also were assumed to be 

constant for the 2004–06 study because no recent data were 

available.

Annual nutrient loads leaving Coeur d’Alene Lake 

in ground-water outflow to the Rathdrum Prairie aquifer 

were computed by multiplying the estimated ground 

water outflow volume, in cubic hectometers, by the mean 

nutrient concentration, in micrograms per liter, in the lower 

hypolimnion of the northern end of Coeur d’Alene Lake. 

Ground water outflow volume was estimated and reported 

as 205 cubic hectometers per year for the 1991–92 study in 

Woods and Beckwith (1997) and was assumed to be constant 

for the 2004–06 study. The mean annual concentration of 

nutrients, in micrograms per liter, in the epilimnion of the 

northern end of the lake was multiplied by the annual change 

in lake volume, in cubic hectometers, to compute the annual 

nutrient load associated with this budget component. Change 

in lake volume was computed separately for each year in both 

studies.

Errors were calculated or estimated for each budget 

component. Standard errors for the load estimates computed 

for the St. Joe, Spokane, and Coeur d’Alene Rivers were 

provided in the LOADEST output as average daily errors for 

each month. These daily errors were multiplied by the number 

of days in each month and were then summed for each year 
Methods 11

in the 1991–92 and 2004–06 studies. Errors for nutrient loads 

from nearshore wastewater and precipitation for the 1991–92 

study were reported in Woods and Beckwith (1997); because 

loads for these budget components were assumed to be 

constant for the 2004–06 study, errors also were assumed to 

be constant. Similarly, errors for nutrient loads from ungaged 

surface-water inflows, ground-water outflows, and lake 

storage change for the 1991–92 study were reported in Woods 

and Beckwith (1997). However, these loads were not assumed 

to be constant for the 2004–06 study. Because loads for these 

budget components in the 2004–06 study were estimated 

using relations with loads from the 1991–92 study, errors were 

assumed to be proportional. An average percent error relative 

to a load was calculated for the 1991–92 study and applied to 

the 2004–06 load estimates. For example, the average percent 

error (error divided by the associated load, in percent) in total 

nitrogen load in ground-water outflow for the 1991–92 study 

was 25 percent. Errors in total nitrogen loads in ground-water 

outflow for each year in the 2004–06 study were calculated 

by multiplying the annual load by the average percent error 

in the 1991–92 study (25 percent). Because recent data were 

unavailable to calculate loads for some budget components, 

reported errors for the 2004–06 study may not be accurate.

Overall error for each nutrient and trace metal budget was 

computed using the following equation (Brown, 1987):

OE = ((E1)2 + (E2)2 + ... + (En)2)0.5, (5)

where:

OE is the overall standard error associated with each 

nutrient or trace metal budget, in kilograms; and

En is the total standard error associated with each budget 

component, in kilograms.

Depth Profiles and Nutrient Sample Collection

Status and trends of lake productivity indices such 

as water-column transparency, nitrogen and phosphorus 

concentrations, chlorophyll-a concentrations, and dissolvedoxygen concentrations were evaluated using limnological 

data. Water-column circulation processes also were evaluated 

on the basis of spatial and temporal changes in nutrients, 

chlorophyll-a, and dissolved-oxygen concentrations.

Prior to collecting water samples at the pelagic stations, 

full-depth profiles of the water column were measured for 

temperature, pH, oxidation-reduction potential, specific 

conductance, dissolved oxygen concentration and percent 

saturation, light transmissivity (a surrogate for turbidity), and 

fluorescence (a surrogate for chlorophyll-a). The upper water 

column was profiled for PAR to define the euphotic zone 

depth. Secchi-disc transparency depth was also measured. The 

euphotic zone is the part of the water column in which PAR is 

equal to or greater than 1 percent of the PAR incident on the 

lake surface. Water column samples were collected eight times 

per year at the five pelagic stations. At the deeper stations 

(1, 3, and 4), samples were collected in the euphotic zone 

(composite), upper hypolimnion, mid-hypolimnion, and lower 

hypolimnion (1 m above lakebed). Station 5 was sampled in 

the euphotic zone and upper and lower hypolimnion, whereas 

station 6, the shallowest, was sampled in the euphotic zone 

and lower hypolimnion. The samples were analyzed for total 

concentrations of nitrogen and phosphorus and dissolved 

concentrations of nitrite plus nitrate, ammonia, phosphorus, 

and orthophosphate. The euphotic zone samples also were 

analyzed for concentrations of chlorophyll-a and pheophytin. 

Littoral zone samples were analyzed using the same methods 

as pelagic euphotic zone samples, except only one 2-m-deep 

sample was collected at each station.

Trace Metal Sample Collection

Limnological data were evaluated for the status and 

trends of trace metal concentrations in the lake. Water column 

circulation processes also were evaluated on the basis of 

spatial and temporal changes in trace metal concentrations.

Water column samples for trace metal analyses were 

collected in conjunction with pelagic zone nutrient samples 

during both study periods. The samples from the five pelagic 

stations were analyzed for total and dissolved concentrations 

of cadmium, lead, zinc, iron, and manganese, as well as 

hardness. The lower hypolimnion samples also were analyzed 

for dissolved arsenic. Littoral zone samples were analyzed for 

the same constituents as the pelagic euphotic zone samples, 

except only one 2-m-deep sample was collected at each 

station.

The exchange of constituents between a water column 

of a lake and lakebed sediments, often termed benthic flux, 

has been identified as an important water-quality issue for 

Coeur d’Alene Lake (Horowitz and others, 1993, 1995a, 

1995b; Kuwabara and others, 2000; and Woods, 2004). To 

complement water column sampling and to obtain recent 

information related to the benthic flux of trace metals, 

samples near the sediment-water interface were collected at 

station 4 on each sampling trip during the 2004–06 study. To 

avoid disturbing the thin veneer of flocculent material at the 

sediment-water interface, samples were collected by gentle 

and slow insertion of a modified gravity coring device (with 

non-metallic core tube liner, core cutter, and core catcher) into 

the lakebed sediments. Upon retrieval, the water within 0.1 m 

of the lakebed (but above the flocculent layer) was gently 

removed from the core tube liner using a peristaltic pump. The 

sample was discarded if significant re-suspension of sediment 

was observed or suspected during retrieval. Analyses for 

trace metals and nutrients were the same for these samples as 

the samples from the water column. Analyses also included 

particulate and dissolved organic carbon (DOC). 
12 Coeur d’Alene Lake, Idaho: Insights Gained From Limnological Studies of 1991–92 and 2004–06

Comparison of Limnological Conditions 

Selected limnological variables common to the 1991–92 

and 2004–06 studies were compared to determine changes 

associated with the interaction of physical, chemical, and 

biological processes in Coeur d’Alene Lake. The report on the 

1991–92 study (Woods and Beckwith, 1997) presents detailed 

discussions of historical effects on the water quality in Coeur 

d’Alene Lake and the results of an applied empirical nutrient 

load/lake response model (Walker, 1987) to evaluate the lake 

response to nutrient inputs (Woods and Beckwith, 1997).

Where statistical comparisons are made among sampling 

stations and (or) study periods, various non-parametric 

statistical techniques were used in the NCSS statistical 

software package (Hintze, 2006). The techniques used for 

various data types are:

• Censored data with single or multiple reporting 

limits—A Kaplan-Meier logrank hypothesis test and 

a Peto-Prentice score hypothesis test were used to 

compare analytical values among stations and between 

study periods. These tests assign percentiles to data 

points and compare differences in each sampled 

population’s cumulative distribution function. No 

values are substituted for the censored data. Both 

methods are identified in Helsel (2005) as appropriate 

for use in comparing data sets with multiple reporting 

limits, and both produced identical results in all 

cases. In addition, a lognormal maximum likelihood 

estimator regression method (Helsel, 2005) was used 

to test the significance of changes over time and to 

support the hypothesis tests.

• Uncensored data (all detected values)—A MannWhitney hypothesis test (Helsel and Hirsch, 2002) was 

used to compare analytical values among stations and 

between study periods.

• Paired uncensored data (all detected values)—A 

Wilcoxon Signed-Ranks hypothesis test (Helsel and 

Hirsch, 2002) was used to compare paired analytical 

concentrations:

• Analytical concentrations in samples collected in the 

euphotic zone and hypolimnion for the same station 

and collection date,

• Analytical concentrations in samples collected in the 

lower hypolimnion and sediment-water interface at 

station 4 for the same collection date, and

• Analytical concentrations in samples collected from 

pelagic stations and the closest paired littoral stations 

during the same week.

• Paired censored data—A Wilcoxon Signed-Ranks 

hypothesis test was used to compare paired analytical 

values. In the rare case when the paired test was used 

on censored data, the non-detects were replaced with 

values equal to their reporting limits. In nearly all cases 

where this occurred, both paired values were censored 

and replaced with the same value for the reporting 

limit.

In nearly all cases, data from calendar years 1991 and 

1992 were grouped into one study period referred to as 

“1991–92”. Likewise, data from water years 2004, 2005, 

and 2006 were grouped into one study period referred to as 

“2004–06”. The data were grouped and compared as study 

periods rather than individual years to compare overall 

differences in lake water quality between the two studies.

In all cases, single- and double-tailed hypothesis 

tests were employed at a significance level of α=0.05. A 

double-tailed hypothesis test was first used to determine 

if a significant difference was measured between median 

values in the sampled populations. If a significant difference 

was measured, the single-tailed hypothesis test was used to 

determine which sampled population had a greater median 

value. Where used in this report, the term “significant” 

denotes that the comparison was statistically significant at a 

significance level of α=0.05.

Hydrologic, Nutrient, and Trace Metal Budgets

The fate and transport of water and associated waterquality constituents following their delivery into a lake 

are determined by the interactions of a myriad of physical, 

chemical, and biological processes operating in the lake over a 

wide range of spatial and temporal scales. To evaluate the net 

effects of those processes in a lake, hydrologic and constituent 

budgets can be developed by quantifying water and constituent 

mass entering and exiting the lake. The quantified mass 

inflow or outflow commonly is referred to as a load, which is 

defined as the quantity of a constituent passing a riverine cross 

section per unit of time. Load is calculated as the product of 

constituent concentration and discharge.

Although the calculation of load is simple 

mathematically, the method of deriving concentration 

and discharge can produce substantial differences in load 

calculations, especially for periods longer than 1 day. 

Constituent concentration and discharge vary substantially 

during a year and are nonsynchronous in their temporal 

variation. Concentrations of dissolved and particulate 

constituents respond differently to discharge changes. 

Therefore, constituent loads may vary on a daily, monthly, 

and (or) annual basis. Various basic to complex methods have 

been used to process multiple-date data sets of concentration 
Comparison of Limnological Conditions 13

and discharge into estimates of seasonal and annual loads. One 

basic method is to multiply the mean values of concentration 

and discharge over the period of interest to derive the load. 

Additional temporal resolution can be gained by linear 

interpolation of measured values of concentration and 

discharge to examine daily load variability over the period of 

interest. More complex methods use linear regression, either 

simple or multiple, to relate load or concentration to discharge 

and other explanatory variables such as seasonality and time 

trend.

Constituent loads typically are quite variable within 

and among years because discharge changes often are the 

dominant influence on loads. This is especially true for 

sediment-associated constituents where the sediment supply 

is not limited. In this situation, the smallest loads of sedimentassociated constituents measured during a year typically 

are associated with minimum discharges due to decreased 

water velocities that produce less erosion and transport. 

Alternatively, increased water velocities during maximum 

discharge during a year can result in erosion and transport 

and large loads of sediment-associated constituents. The 

pattern generally is similar for dissolved constituents, but 

differences in loads between high and low discharge are 

decreased because the transport of dissolved constituents is 

less dependent on water velocity. These within-year patterns 

of load variability for sediment-associated and dissolved 

constituents in a lake are important considerations for 

determining the effects on the fate and transport of nutrient 

loads. The transport of seasonal loads also applies to annual 

loads; large constituent loads generally are transported during 

high discharge years than during low discharge years.

Table 4 presents streamflow and nutrient loads from the 

Coeur d’Alene and St. Joe River inflows and the Spokane 

River outflow from Coeur d’Alene Lake determined using 

LOADEST, as well as nutrient load estimates from ungaged 

sources. Robust comparisons among years and load sources 

are limited by the difference in study periods (calendar year 

and water year) and the difference in analytical reporting 

limits between the two studies.

Streamflow for the 5 years varied substantially in 

response to differences in annual runoff from the watershed 

and operation of Post Falls Dam. The annual hydrologic 

conditions for those 5 years in relation to mean hydrologic 

conditions were compared to the long-term annual streamflow 

of the USGS gaging station on the Spokane River near 

Post Falls (USGS gaging station 12419000). The mean 

annual streamflow at Spokane River near Post Falls during 

1912–2006 was 175 m3

/s (U.S. Geological Survey, 2007). In 

comparison, the annual mean streamflows for calendar years 

1991 and 1992 and water years 2004, 2005, and 2006 were, 

199, 99, 131, 134, and 186 m3/s, respectively. Therefore, the 

percentages of long-term annual mean streamflow among the 

5 years were 113, 56, 74, 76, and 106, respectively. Because 

streamflow is a key factor in the calculation of constituent 

load, the different hydrologic conditions among the 5 years 

were responsible for most differences in annual loads 

delivered into and discharged out of Coeur d’Alene Lake. 

The residual for each nutrient load (nitrogen or 

phosphorus) was computed as the sum of total outflow loads 

minus the sum of total inflows and is presented in table 4. 

The residual also is presented as a percentage of the total 

inflow load. Although the residual can be considered roughly 

the amount of nutrient load retained in the lake, the estimate 

contains errors associated with measured and unmeasured 

budget components. Unquantifiable uncertainties exist in these 

residual estimates because nutrients in Coeur d’Alene Lake 

are affected to an unknown degree by physical, chemical, and 

biological processes.

Total nitrogen inflow and outflow loads decreased 

between the 1991–92 and 2004–06 study periods. The St. 

Joe River contributed the largest percentage of inflow total 

nitrogen load in 1991 (47 percent), and the Coeur d’Alene 

River contributed slightly higher total nitrogen loads than 

the St. Joe River in other years studied. Combined, the St. 

Joe and Coeur d’Alene Rivers contributed an average of 82 

percent of the total inflow nitrogen load in the 1991–92 study, 

but an average of only 40 percent of the total inflow nitrogen 

load in the 2004–06 study. Estimated inputs from ungaged 

tributaries and other surface-water inflows constitute a larger 

percentage of the inflow total nitrogen load in the 2004–06 

study (36–46 percent) compared with the 1991–92 study 

(11–13 percent). Reductions in total nitrogen in the St. Joe and 

Coeur d’Alene Rivers were expected due to reductions in total 

nitrogen concentrations and loads in municipal wastewater 

effluent. For example, effluent monitoring reports from the 

Coeur d’Alene municipal wastewater treatment plant, which 

is typical of other wastewater treatment plants on the St. Joe 

and Coeur d’Alene Rivers, show an increase in total nitrogen 

removal efficiency from 16 to 56 percent between the 1991–92 

and 2004–06 study periods due to improvements in treatment 

processes. Nutrients in ungaged tributaries and other surfacewater inflows were expected to be from untreated wastewater, 

agriculture, and natural sources. Nutrient concentrations in 

these inflows were assumed to be relatively constant between 

the 1991–92 and 2004–06 studies and, therefore, constituted 

a larger percentage of the overall inflow total nitrogen load 

in the latter study. Additional measurements to quantify loads 

from ungaged tributaries, as well as other ungaged inflows 

and outflows including nearshore wastewater, precipitation, 

ground water, and lake storage changes, would improve load 

estimates and verify assumptions. Load estimates presented 

in table 4 for ground-water outflow and lake storage change 

in the 1991–92 study differ slightly from estimates published 

in Woods and Beckwith (1997) due to a small error in the 

calculations used to generate those estimates. The Spokane 

River is the dominant outflow route of total nitrogen from 

Coeur d’Alene Lake (85-95 percent of total outflow).
14 Coeur d’Alene Lake, Idaho: Insights Gained From Limnological Studies of 1991–92 and 2004–06

Variable Budget component Calendar year Water year

1991 1992 2004 2005 2006

Streamflow St. Joe River 3,350 1,660 1,940 2,140 2,720

Coeur d’Alene River 2,610 1,280 1,700 1,910 2,550

Spokane River 6,270 3,140 4,120 4,230 5,870

Load Error Load Error Load Error Load Error Load Error

Total nitrogen

Inflow St. Joe River 991,000 98,000 343,000 26,100 62,700 18,500 48,500 16,600 84,600 28,600

Coeur d’Alene River 819,000 93,600 402,000 36,800 117,000 11,600 107,000 12,800 87,900 12,000

Ungaged tributaries 

and other surfacewater inflow

225,000 46,400 128,000 28,500 148,000 31,100 164,000 34,400 214,000 44,900

Nearshore wastewater 4,900 1,220 4,900 1,220 4,900 1,220 4,900 1,220 4,900 1,220

Precipitation 75,000 11,500 75,000 11,000 75,000 11,200 75,000 11,200 75,000 11,200

Outflow Spokane River 1,670,000 107,000 709,000 38,300 217,000 54,300 181,000 45,200 597,000 253,000

Ground-water outflow 

to Rathdrum Prairie

71,500 17,900 54,300 13,600 33,300 8,320 28,700 7,180 40,500 10,100

Lake storage change 9,710 850 11,500 860 2,320 190 3,640 290 1,540 120

Total phosphorus

Inflow St. Joe River 40,100 11,100 14,800 3,400 35,300 3,670 45,100 5,150 71,600 8,690

 Coeur d’Alene River 33,600 6,480 10,900 1,600 25,700 4,060 38,200 7,260 54,200 9,860

 Ungaged tributaries 

and other surfacewater inflow

12,200 2,340 6,850 1,570 7,960 1,670 8,860 1,860 11,500 2,420

Nearshore wastewater 390 100 390 100 390 100 390 100 390 100

Precipitation 6,460 1,000 6,460 1,100 6,460 1,050 6,460 1,050 6,460 1,050

Outflow Spokane River 46,600 7,320 24,800 3,360 32,200 4,480 31,500 4,040 52,000 9,120

Ground-water outflow 

to Rathdrum Prairie

1,000 250 510 130 990 250 1,190 300 3,250 810

Lake storage change 180 10 130 30 180 20 180 20 80 20

Summary

Constituent load Calendar year Water year

1991 1992 2004 2005 2006

Total nitrogen

Total inflow 2,110,000 953,000 408,000 399,000 466,000

Total outflow 1,750,000 775,000 253,000 213,000 639,000

Residual (outflow- inflow) -360,000 -178,000 -155,000 -186,000 173,000

Residual (percentage of inflow) 17 19 38 47 NA

Overall error 180,000 68,000 67,700 62,000 259,000

Total phosphorus

Total inflow 92,800 39,400 75,800 99,000 144,000

Total outflow 47,800 25,400 33,400 32,900 55,300

Residual (outflow- inflow) -45,000 -14,000 -42,400 -66,100 -88,700

Residual (percentage of inflow) 48 36 56 67 62

Overall error 15,000 5,400 7,350 10,000 16,200

Table 4. Nutrient load budgets and errors, Coeur d’Alene Lake, Idaho, calendar years 1991–92 and water years 2004–06.

[Sampling locations are shown in figure 1. Sampling locations on the St. Joe and Spokane Rivers changed between the 1991–92 and 2004–06 studies. For 

comparability, data are normalized to the following stations: St. Joe River: USGS gaging station 12415140, St. Joe River near Chatcolet; Spokane River, USGS 

gaging station 12417598, Spokane River at Lake Outlet at Coeur d’Alene. Sampling location on the Coeur d’Alene River for both studies was at USGS gaging 

station 12413860, Coeur d’Alene River near Harrison. Load and error estimates for ungaged tributaries and other surface-water inflow in 1991 and 1992 are 

from Woods and Beckwith (1997). Loads for ungaged tributaries and other surface-water inflow in 2004–06 were estimated using a relation between 1991–92 

load data and annual flow in closest gaged tributary (see text for full explanation). Load and error estimates for nearshore wastewater and precipitation in 1991 

and 1992 are from Woods and Beckwith (1997). Assumed nearshore wastewater and precipitation loads and errors were constant for 2004–06 study as no recent 

data were available. Actual error unknown for loads from ungaged tributaries, surface-water inflow, ground-water outflow, and lake storage change in 2004–06 

study. Errors for 2004–06 were estimated by applying the average percent error in loads from the 1991–92 study (see text for full explanation). Loads and errors 

are in kilograms per year. Streamflows are in cubic hectometers per year. Abbreviations: USGS, U.S. Geological Survey; NA, not applicable]
Comparison of Limnological Conditions 15

Total nitrogen was retained in the lake in all years studied 

except water year 2006, when the residual was positive, 

indicating a higher outflow than inflow of total nitrogen load. 

However, the residual is less than the overall error in the total 

nitrogen budget for 2006, and inflow and outflow loads of 

total nitrogen most likely were equal. Residuals for all other 

years were larger than the overall corresponding errors and 

ranged from 17 to 47 percent of the total inflow load.

Total phosphorus inflow and outflow loads fluctuated 

with streamflow in both study periods, but loads relative 

to streamflow were higher in the 2004–06 study than the 

1991–92 study because total phosphorus concentrations in 

gaged inflows were statistically higher in the latter study. 

The St. Joe River contributed the largest percentage of inflow 

total phosphorus load (38–50 percent) in all years studied. 

The Coeur d’Alene River was the second largest source, 

contributing 28–39 percent of the inflow total phosphorus 

load. Combined, the percent contributions to inflow load 

from the St. Joe and Coeur d’Alene Rivers were relatively 

consistent across both study periods (72 percent in the 

1991–92 study and 84 percent in the 2004–06 study). Ungaged 

tributaries and other surface-water inflow comprised the third 

largest source, contributing 8–13 percent of the inflow total 

phosphorus load. As with total nitrogen, total phosphorus 

loads in outflow of the Spokane River (94–98 percent) 

dominated other outflow routes.

Total phosphorus was retained in the lake in all years 

studied, and the residuals, expressed as a percentage of inflow, 

were slightly higher in the 2004–06 study than the 1991–92 

study. Residuals for all years were larger than the overall 

corresponding errors and ranged from 36 to 67 percent of total 

inflow load.

Table 5 presents selected trace-metal loads from the 

Coeur d’Alene and St. Joe River inflows and the Spokane 

River outflow determined using LOADEST. Robust 

comparisons among years and load sources were hampered 

by differences in study periods (calendar year and water 

year), in analytical reporting limits between the two studies, 

and in sampling locations on the St. Joe and Spokane Rivers, 

which were not normalized for the trace-metal load budget. 

Total cadmium loads could not be calculated for the St. Joe 

River using LOADEST because total cadmium concentrations 

frequently were less than the method reporting limit.

The largest loads of the three constituents presented (total 

cadmium, total lead, and total zinc) occurred in 1991, the 

year of the highest streamflows (table 4). Samples collected 

in the 2004–06 study at gaging stations on the St. Joe and 

Spokane Rivers indicated reductions in loads because the trace 

metal concentrations were within the range of differences in 

analytical reporting limits used during the two studies. The 

reporting limit was lowered and more uncensored data points 

were available for the LOADEST calculations in the 2004–06 

study than in the 1991–92 study. Trace metal concentrations 

for the Coeur d’Alene River exceeded analytical reporting 

limits used in both studies; therefore, loads at that station 

were least affected by those differences. The Coeur d’Alene 

River was, by far, the largest source of trace metal loads to the 

lake. Combining both study periods, the Coeur d’Alene River 

contributed an average of 100 percent of total cadmium and 

97 percent of total lead and total zinc gaged inflow loads.

An important comparison can be made based on the 

relative magnitude of constituent loads delivered into the 

lake as opposed to those discharged out of the lake. The 

sum of loads from the Coeur d’Alene and St. Joe Rivers 

was compared to the load at the Spokane River (lake outlet), 

for total cadmium, total lead, and total zinc (table 5). The 

retention of the three constituents in the lake, expressed as 

the residual as a percentage of inflow, was slightly higher in 

the 2004–06 study period than in the 1991–92 study period. 

However, not all inflows to the lake could be quantified, 

and reported residuals may be lower than actual values. 

The percentage of total cadmium retained ranged from 36 

to 70. A larger percentage of total lead was retained by the 

lake, ranging from 83 to 96. These high residuals reflect the 

propensity of lead to be associated with sediment particles 

and to be prone to sedimentation in the lake. Zinc is the most 

soluble of the three trace metals, and the percentage retention 

in the lake ranged from 33 to 52. Relative to loads, higher 

errors were present in lead and zinc load estimates for the St. 

Joe River compared to the Coeur d’Alene and Spokane Rivers.

Water Temperature and Water Column 

Transparency

The physical limnological processes of thermal 

stratification and convective circulation are strongly 

correlated with the vertical distribution of water-quality 

properties and constituents. Thermal structure in some lakes 

may be established, in part, by riverine inflows. However, 

the major source of heat for most lakes is the short- and 

long-wave radiation that impinges on the surface of a lake 

(Wetzel, 1983). Wind energy distributes the surface heat 

into the water column until density differences impede 

deeper mixing. In lakes deep enough to resist full-depth 

convective circulation, solar heating and wind mixing during 

the summer vertically segregate the water column into three 

zones: epilimnion, metalimnion, and hypolimnion. The upper 

zone, the epilimnion, is the stratum in which most biological 

production occurs because light generally is sufficient to 

drive photosynthetic production by phytoplankton. The 

metalimnion is the stratum of maximum temperature change; 

density differences may be sufficient to impede settling of 

detrital material into the lower stratum, the hypolimnion. A 

thermocline is present within the metalimnion if the rate of 

temperature change exceeds 1o

C/m. The hypolimnion, which 

overlies the lakebed sediments, typically is more thermally 

stable than the epilimnion or metalimnion. During thermal 
16 Coeur d’Alene Lake, Idaho: Insights Gained From Limnological Studies of 1991–92 and 2004–06

Variable Budget component

Calendar year Water year

1991 1992 2004 2005 2006

Load Error Load Error Load Error Load Error Load Error

Total cadmium

Gaged inflow St. Joe River ND NA ND NA ND NA ND NA ND NA

Coeur d’Alene River 8,930 1,070 4,170 460 2,300 270 3,090 420 3,300 440

Gaged outflow Spokane River 5,720 680 2,560 290 1,000 60 930 50 1,270 90

Total lead

Gaged inflow St. Joe River 34,400 9,300 5,860 1,300 380 70 530 130 740 160

Coeur d’Alene River 488,000 111,000 74,400 11,000 85,400 13,600 111,000 22,100 178,000 32,800

Gaged outflow Spokane River 68,200 9,300 13,400 1,510 5,540 640 5,050 570 6,520 1,160

Total zinc

Gaged inflow St. Joe River 59,900 18,000 39,300 11,000 2,870 500 3,830 760 5,190 840

Coeur d’Alene River 935,000 127,000 444,000 52,200 367,000 46,000 482,000 69,200 552,000 77,400

Gaged outflow Spokane River 648,000 50,800 324,000 23,100 240,000 7,630 235,000 8,060 309,000 12,900

Summary

Constituent load

Calendar year Water year

1991 1992 2004 2005 2006

Total cadmium

Total inflow 8,930 4,170 2,300 3,090 3,300

Total outflow 5,720 2,560 1,000 930 1,270

Residual (outflow-inflow) -3,210 -1,610 -1,300 -2,160 -2,030

Residual (percentage of inflow) 36 39 56 70 62

Overall error 1,270 540 280 420 450

Total lead

Total inflow 522,000 80,300 85,800 112,000 179,000

Total outflow 68,200 13,400 5,540 5,050 6,520

Residual (outflow-inflow) -454,000 -66,900 -80,300 -107,000 -172,000

Residual (percentage of inflow) 87 83 94 95 96

Overall error 112,000 11,200 13,600 22,100 32,800

Total zinc 

Total inflow 995,000 483,000 370,000 486,000 557,000

Total outflow 648,000 324,000 240,000 235,000 309,000

Residual (outflow-inflow) -347,000 -159,000 -130,000 -251,000 -248,000

Residual (percentage of inflow) 35 33 35 52 44

Overall error 138,000 58,100 46,600 69,700 78,500

Table 5. Selected trace-metal loads and errors measured at three gaging stations near Coeur d’Alene Lake, Idaho, calendar years 

1991–92 and water years 2004–06.

[Sampling locations are shown in figure 1. Sampling locations on the St. Joe and Spokane Rivers changed between the 1991–92 and 2004–06 studies. Few 

differences in trace-metal inputs are expected between sampling locations. Locations sampled in 1991–92 study: St. Joe River, USGS gaging station 12415075, 

St. Joe River at St. Maries; Spokane River, USGS gaging station 12419000, Spokane River near Post Falls. Locations sampled in 2004–06 study: St. Joe, 

USGS gaging station 12415140, St. Joe River near Chatcolet; Spokane River, USGS gaging station 12417598, Spokane River at Lake Outlet at Coeur d’Alene. 

Sampling location on the Coeur d’Alene River for both studies was at USGS gaging station 12413860, Coeur d’Alene River near Harrison. Loads and errors are 

in kilograms per year. Streamflows are in cubic hectometers per year. Abbreviations: ND, analyte concentration frequently less than method reporting limit; 

unable to calculate loads using LOADEST; USGS, U.S. Geological Survey ; NA, not applicable]
Comparison of Limnological Conditions 17

0

4

8

12

16

1991-92

2004-061991-922004-061991-922004-061991-922004-061991-922004-06

PELAGIC STATIONS AND YEARS

MEDIAN DEPTH, IN METERS

Station 1 Station 3 Station 4 Station 5 Station 6 No data

Thermocline

Secchi-disc

 transparency

Euphotic zone

Figure 3. Median depths of thermocline, Secchi-disc 

transparency, and euphotic zone at five pelagic stations, 

Coeur d’Alene Lake, Idaho, calendar years 1991–92 and 

water years 2004–06.

stratification, the hypolimnion is isolated from atmospheric 

exchange and may develop a dissolved oxygen deficit if 

biological and chemical oxygen demands exceed the oxygen 

mass available within the hypolimnion at the onset of thermal 

stratification. During spring and autumn, solar radiation 

input is less than during summer, and windy conditions often 

are more prevalent. This combination facilitates convective 

circulation, the process whereby a weakly stratified water 

column undergoes vertical mixing when wind energy is 

sufficient to overcome the thermal gradient. A lake is termed 

dimictic if it undergoes convective circulation throughout 

its water column in spring and autumn. Such mixing is an 

important mechanism for the vertical movement of waterquality constituents such as dissolved oxygen, nutrients, and 

trace metals.

Heating of Coeur d’Alene Lake during the 1991–92 

and 2004–06 studies produced annual maximum water 

temperatures within 1.2oC among the 5 years compared. The 

maximum water temperature measured during 1991 was 

23.4oC at station 6 during early August and, during 1992, 

23.2oC at station 6 during late June (Woods and Beckwith, 

1997; appendix A). Maximum water temperatures for 2004, 

2005, and 2006 were 22.6oC (station 6, mid-July), 22.2oC 

(station 6, mid-July), and 22.4oC (station 4, mid-August), 

respectively (appendix B).

These similarities in maximum water temperatures did 

not result in similar thermocline depths among the stations for 

the 5 years. The median thermocline depths for stations 1, 3, 

4, 5, and 6 during the two study periods ranged from 5.5 m at 

station 6 in 2004–06 to 13 m at station 1 in 1991–92 (fig. 3). 

At each station, median thermocline depths varied by as 

little as 1.5 m (station 6) and by as much as 3.5 m (station 5). 

These differences reflect numerous influences on a location’s 

propensity to stratify thermally; important influences include 

depth, exposure to wind, proximity to riverine inflows, and 

exposure to internal waves at the thermocline (Woods, 2004).

The development and breakdown of thermal stratification 

have important consequences for the fate and transport of 

constituents in lakes. At the deep stations in Coeur d’Alene 

Lake (stations 1, 3, and 4), thermal stratification (depicted 

by the presence of a thermocline) developed by mid-July and 

persisted until early October 1991. In 1992, the thermocline 

developed by June and persisted until mid-October (Woods 

and Beckwith, 1997, fig. 9). During 2004, thermoclines 

developed by mid-June and persisted into mid-October, 

except at station 4 where the thermocline disappeared prior 

to the October sampling trip (appendix B). The thermoclines 

at stations 3 and 4 developed in mid-June 2005, following 

an earlier development in late May at station 1; thermoclines 

at these three stations disappeared by early October 

(appendix B). During 2006, thermoclines developed by 

mid-June and persisted into mid- October, except at station 

4 which was not sampled during the October sampling trip 

(appendix B). The thermocline at station 4 was detected in late 

August.

Water column transparency was characterized as Secchidisc transparency depth and euphotic zone depth, both of 

which are shown in figure 3 as median values for each station 

for the two study periods. The smallest medians for both 

variables were measured at station 6, the shallowest of the five 

stations and the most exposed to turbid riverine inflows from 

the St. Joe River. The three deep stations had similar median 

values although the largest values for Secchi-disc transparency 

depth were recorded at station 1, the farthest from riverine 

inflows. The variation of euphotic zone depth among the five 

stations was similar to that of Secchi-disc transparency depth. 

Some lack of correspondence between the two variables at 

a station likely is due to the subjective nature of measuring 

Secchi-disc transparency depth.

The foregoing comparison of water temperatures and 

water column transparency among the study periods and 

the five stations indicated no substantive changes in water 

column heating and convective circulation because heating 

and circulation are largely driven by physical limnological 

processes, which have not changed at Coeur d’Alene Lake. 

Anthropogenically induced changes in sediment delivery 

to the lake and (or) increased phytoplankton productivity 

have the potential to affect water column transparency. No 

such effects were detected with these data. A longitudinal 

gradient exists from south (low transparency) to north (high 

transparency) as a consequence of turbid riverine inflows 

entering the lake from the south.
18 Coeur d’Alene Lake, Idaho: Insights Gained From Limnological Studies of 1991–92 and 2004–06

Dissolved Oxygen Concentration and 

Percent Saturation

The concentration of dissolved oxygen in water is 

affected by temperature, barometric pressure, oxygen 

production by photosynthesis, oxygen consumption by 

respiration and decomposition, exchange across the airwater interface, and mixing (Hem, 1985). The temporal and 

spatial distributions of dissolved-oxygen concentrations in 

lakes are important indices of water quality. However, some 

effects described earlier in this report concealed important 

processes that can be better evaluated with the variable percent 

saturation of dissolved-oxygen concentration, defined here as 

the ratio (expressed as a percentage) of measured dissolvedoxygen concentration to that which would exist under 

saturated conditions at the same temperature.

During the 1991–92 study, the overall range in dissolvedoxygen concentrations over depth and time among the pelagic 

stations was 0 to 13.6 mg/L; both extremes were measured 

at station 6 (Woods and Beckwith, 1997; appendix A). The 

overall range in dissolved oxygen concentrations during 

2004–06 was 0.2 to 13.7 mg/L with the minimum measured at 

station 6 and the maximum at station 1 (appendix B). Over the 

two study periods, the highest concentrations at each station 

were measured in the winter in association with minimum 

water temperatures confirming the inverse relation between 

dissolved-oxygen concentration and temperature. Minimum 

concentrations were measured in the hypolimnia of each 

station during late summer or autumn as prolonged thermal 

stratification restricted mixing of the oxygenated upper water 

column with the hypolimnion.

Ranges for the percent saturation of dissolved-oxygen 

concentrations for the 5 stations during the study periods are 

plotted in figure 4. Wider ranges and smaller minimum values 

were recorded at stations 5 and 6. Station 6 attained anoxic 

or near-anoxic conditions in each year; station 5 percent 

saturations were as low as 24 in the 2004–06 study. Similar 

minimum percent saturations, ranging from 54 to 65, were 

recorded at the three deep stations (1, 3, and 4), which have 

not shown hypolimnetic anoxia.

Saturations greater than 100 percent were measured at 

all stations in 4 or more of the 5 years. These saturations were 

associated with the euphotic zone during the summer months 

when photosynthetic-oxygen production exceeded oxygen 

consumption processes. The minimum percent saturations 

were in the hypolimnia of the stations during late summer or 

autumn.

A statistical analysis of dissolved-oxygen concentrations 

and percent saturations among the two study periods and five 

stations (tested separately) indicated no significant change 

between study periods. At all stations, median dissolvedoxygen concentrations were significantly lower in the 

hypolimnion than in the euphotic zone. Median concentrations 

were significantly lower at stations 5 and 6 than at all other 

stations for both study periods. A significant longitudinal 

gradient in the loss of dissolved oxygen is apparent from north 

to south. However, that gradient is mostly a consequence 

of the shallow depths and higher biological productivity at 

stations 5 and 6.

Total Phosphorus

Phosphorus is one of several essential nutrients in the 

metabolism of phytoplankton and aquatic plants and was 

measured in both studies. Eutrophication research has focused 

heavily on phosphorus, the nutrient often having the smallest 

supply-to-demand ratio for aquatic plant growth (Ryding and 

Rast, 1989). Phosphorus concentrations for both studies were 

reported as total phosphorus and dissolved orthophosphate 

(dissolved phosphorus also was reported for the 2004–06 

study). Total phosphorus represents phosphorus in solution 

(dissolved or colloidal) and phosphorus contained in or 

attached to biotic and abiotic particulate material. Dissolved 

phosphorus and orthophosphate are determined from the 

filtrate that passes through a filter with a nominal pore size of 

0.45 μm.

The comparison of phosphorus focused on total 

phosphorus because analytical method reporting limits for 

dissolved orthophosphate differed between the two studies, 

resulting in numerous non-detected orthophosphate values 

in the 2004–06 study. Table 6 presents changes in method 

reporting limits and number of non-detected values in the 

1991–92 and 2004–06 studies for relevant constituents, 

including dissolved orthophosphate. During the 1991–92 

0

20

40

60

80

100

120

140

1991-92

2004-06

1991-92

2004-06

1991-92

2004-06

1991-92

2004-06

1991-92

2004-06

PELAGIC STATIONS AND YEARS

SATURATION OF DISSOLVED 

OXYGEN CONCENTRATION, IN PERCENT

Station 1 Station 3 Station 4 Station 5 Station 6

Minimum

Maximum

100 percent

Figure 4. Minimum and maximum percent saturation of 

dissolved oxygen at five pelagic stations, Coeur d’Alene 

Lake, Idaho, calendar years 1991–92 and water years 

2004–06.
Comparison of Limnological Conditions 19

study, the method reporting limit for dissolved orthophosphate 

was 1 μg/L; mean concentrations over the 2 years were 

slightly more than 1 μg/L (Woods and Beckwith, 1997), but 

median concentrations at all pelagic stations except station 

6 were less than 1 μg/L. The more rigorous statistical basis 

for method reporting limits (Childress and others, 1999) 

applied during the 2004–06 study resulted in a reporting limit 

of 6 μg/L. About 78 percent of dissolved orthophosphate 

analyses in the 2004-06 study were non-detected values, 

and lake-wide median orthophosphate concentrations at all 

pelagic stations in the 2004–06 study were non-detected 

values, less than 6 μg/L. Therefore, statistical comparisons 

were made only for total phosphorus. The comparisons were 

made using the Kaplan-Meier logrank and Peto-Prentice score 

tests, incorporating the multiple reporting limits for total 

phosphorus.

Total phosphorus concentrations among the pelagic 

stations ranged from less than 1 to 192 μg/L during 1991–92 

(Woods and Beckwith, 1997; appendix A). The largest 

concentration measured was under anoxic conditions within 

the hypolimnion of station 6 during September 1991. Total 

phosphorus concentrations for 2004–06 ranged from 2 

(estimated) to 168 μg/L with the largest concentration from 

the anoxic hypolimnion of station 6 during August 2006 

(appendix B). Median concentrations of total phosphorus 

within the euphotic zone and hypolimnion of each station 

for both study periods are shown in figure 5. A significant 

longitudinal gradient is evident from south to north, with 

higher concentrations associated with the two shallower, 

southern stations. When grouped by study, total phosphorus 

concentrations were significantly higher in the euphotic zone 

and hypolimnion in the 2004–06 study than in the 1991–92 

study at all pelagic stations, which corresponds with the 

increase in total phosphorus loads and concentrations in 

inflows from the Coeur d’Alene and St. Joe Rivers.

The differences in median concentrations of total 

phosphorus between euphotic zone and hypolimnion at each 

station (fig. 5) reveal that water quality differed at the three 

deeper stations than the two shallower stations. During each 

study period, statistically similar concentrations for the two 

depth zones were detected at the deeper stations (1, 3, and 

4). In most cases the difference was only 1 μg/L or less. In 

contrast, the concentration differences between the euphotic 

zone and hypolimnion of stations 5 and 6 ranged from 2.5 to 

3 μg/L and from 5.5 to 7 μg/L, respectively. The hypolimnetic 

phosphorus concentrations at stations 5 and 6 significantly 

exceeded those of their euphotic zones in all cases.

Higher median concentrations of total phosphorus 

within the euphotic zones and hypolimnia of stations 5 and 6, 

compared to the concentrations detected at the deeper pelagic 

stations, reflect several processes. Seasonal anoxia at station 6 

releases dissolved constituents such as phosphorus, nitrogen, 

iron, and manganese from lakebed sediments and detrital 

material within the water column. Additionally, both stations 

are within the inflow plume of the St. Joe River, which is a 

primary source of phosphorus for the lake.

Total phosphorus was not detected in any of the blank 

samples submitted during the 2004–06 study; therefore, 

decontamination procedures were considered adequate to 

remove this constituent from sampling equipment. Mean 

Table 6. Changes in method reporting limits for selected constituents sampled in Coeur d’Alene Lake, Idaho, calendar years 1991–92 

and water years 2004–06.

[Abbreviations: μg/L, microgram per liter; MRL, method reporting limit]

Constituent

Study

1991–92 2004–06

MRL 

(μg/L)

Number of 

analyses

Number 

of nondetected 

values

Percent 

nondetected 

values

MRL 

(μg/L)

Number of 

analyses

Number 

of nondetected 

values

Percent 

nondetected 

values

Total phosphorus 1.0 325 34 10 4.0 402 2 0.50

Dissolved orthophosphate 1.0 323 182 56 6.0 404 314 78

Total ammonia plus organic nitrogen 200 312 244 78 60 403 1 .25

Dissolved inorganic nitrogen 7.0 327 9 2.8 26 404 63 16

Dissolved nitrite plus nitrate 5.0 327 61 19 16 404 90 22

Dissolved ammonia 2.0 327 32 10 10 404 189 47

Total cadmium 1.0 126 117 93 .040 404 44 11

Total lead 1.0 126 30 24 .060 404 1 .25

Total zinc 10 126 17 13 2.0 402 11 2.7
20 Coeur d’Alene Lake, Idaho: Insights Gained From Limnological Studies of 1991–92 and 2004–06

relative standard deviation, a measure of variability induced 

during sample processing and analysis, was 12 percent for 

total phosphorus, based on replicate sample data collected 

during the 2004–06 study. Most of the high relative 

standard deviations were for samples with total phosphorus 

concentrations less than 10 μg/L. At these concentrations, 

small differences between concentrations in replicate and 

routine samples can inflate the relative standard deviation. 

Total phosphorus concentrations in 38 percent of the replicate 

samples matched exactly with corresponding routine samples. 

Selected analytical data for quality control samples collected 

during the 2004–06 study are provided in appendix C.

Dissolved Inorganic Nitrogen

Nitrogen, like phosphorus, is essential to the metabolism 

of aquatic biota. In Coeur d’Alene Lake, the supply-to-demand 

ratio of nitrogen is small (but typically not as small as that of 

phosphorus); thus nitrogen may limit the growth of aquatic 

plants. The nitrogen cycle in aquatic ecosystems is complex 

because nitrogen can assume many redox states and chemical 

forms, and because most processes involving nitrogen are 

biologically mediated. In aquatic ecosystems, nitrogen 

commonly exists as dissolved molecular nitrogen, nitrogencontaining organic compounds, ammonia, nitrite, and nitrate. 

Nitrogen concentrations for the two studies generally were 

reported as total nitrogen and dissolved inorganic nitrogen. 

Total nitrogen represents the sum of ammonia, organic 

nitrogen, nitrite, and nitrate in solution (dissolved or colloidal) 

and contained in or attached to biotic and abiotic particulate 

material. Dissolved inorganic nitrogen represents the sum 

of ammonia, nitrite, and nitrate and is determined from the 

filtrate that passes through a filter with a nominal pore size of 

0.45 μm.

Comparisons involving nitrogen focused on dissolvedinorganic nitrogen concentrations because analytical method 

reporting limits for total-nitrogen concentrations differed 

greatly between the two studies. The method reporting limit 

for total nitrogen during 1991–92 was 205 μg/L (200 μg/L for 

total ammonia plus organic nitrogen and 5 μg/L for dissolved 

nitrite plus nitrate [table 6]); as such, nearly all total nitrogen 

concentrations in Coeur d’Alene Lake were reported as less 

than 205 μg/L for that period. Improved analytical methods 

prior to the 2004–06 study lowered the reporting limit to 

60 μg/L. This change effectively negated the ability to make 

comparisons of total nitrogen between the two studies.

Method reporting limits for dissolved nitrite plus nitrate 

and dissolved ammonia also differed between the two studies 

as shown in table 6; however, the incidence of concentrations 

less than the reporting limit was much less than for total 

nitrogen. During the 1991–92 study, method reporting limits 

were 5 and 2 μg/L as nitrogen for dissolved nitrite plus nitrate 

and dissolved ammonia, respectively. During the 2004–06 

study, a more rigorous statistical basis for method reporting 

limits (Childress and others, 1999) resulted in reporting limits 

of 16 and 10 μg/L as nitrogen, respectively, for dissolved 

nitrite plus nitrate and dissolved ammonia.

Dissolved inorganic nitrogen concentrations among 

the pelagic stations ranged from less than 7 to 332 μg/L 

(320 μg/L of which was ammonia) during 1991–92 (Woods 

and Beckwith, 1997). The largest concentration was measured 

under anoxic conditions within the hypolimnion of station 

6 during September 1991. The dissolved inorganic nitrogen 

concentrations for 2004–06 ranged from less than 21 to about 

265 μg/L (249 μg/L of which was ammonia), with the largest 

concentration from the anoxic hypolimnion of station 6 during 

late August 2004.

Median concentrations of dissolved inorganic nitrogen 

within the euphotic zone and hypolimnion of each station are 

shown in figure 6. Due to an increase in method reporting 

limits for the 2004–06 study, median concentrations in 

the euphotic zone for 2004–06 were less than 26 μg/L 

at all five stations. Unlike median total phosphorus 

concentrations in the euphotic zone (fig. 5), no distinct 

longitudinal gradient for median concentrations of dissolved 

inorganic nitrogen was evident over the five stations in the 

euphotic zone (fig. 6). However, such a gradient did exist 

for hypolimnetic concentrations (fig. 6). The three deep 

stations had significantly higher median concentrations of 

dissolved inorganic nitrogen than did stations 5 and 6, with 

station 4 having the highest median concentrations. Median 

hypolimnetic concentrations for the three deep stations ranged 

Figure 5. Median concentrations of total phosphorus 

in the euphotic zone and hypolimnion at five pelagic 

stations, Coeur d’Alene Lake, Idaho, calendar years 

1991–92 and water years 2004–06.

e 05

0

5

10

15

20

25

30

1991-922004-061991-92

2004-06

1991-92

2004-061991-922004-061991-922004-06

PELAGIC STATIONS AND YEARS

TOTAL PHOSPHORUS CONCENTRATION, 

IN MICROGRAMSPER LITER 

Station 1 Station 3 Station 4 Station 5 Station 6

Euphotic zone

Hypolimnion
Comparison of Limnological Conditions 21

from 80 μg/L (station 1 in 2004–06) to 106 μg/L (station 4 

in 1991–92). In contrast, the range for median hypolimnetic 

concentrations at stations 5 and 6 was from 30 μg/L (station 6 

in 1991–92) to 58 μg/L (station 5 in 2004–06).

The significant differences in median concentrations 

of dissolved inorganic nitrogen between the euphotic zone 

and hypolimnion of the three deep stations (fig. 6) were 

attributable to several limnological processes. The greater 

depth of stations 1, 3, and 4 decreased the frequency of 

convective circulation and allowed development of waterquality stratification during summer. Phytoplanktonic 

assimilation of dissolved inorganic nitrogen decreased 

summertime concentrations within the euphotic zone 

(Woods, 2004); this process also occurred at stations 5 and 

6. Additionally, the highest loads and concentrations of 

dissolved inorganic nitrogen were delivered to the lake during 

winter months, when inflow plumes travel through the lake as 

underflow. As lower-concentration inflows in other seasons 

flushed through the lake as overflow or interflow, some higher 

concentration contributions may have been trapped throughout 

the year in the deeper areas of the lake. The process of benthic 

flux likely served to enrich hypolimnetic concentrations at the 

deeper stations as well as station 5.

No significant temporal changes were detected in 

hypolimnetic dissolved inorganic nitrogen between study 

periods at any pelagic station. A statistical comparison in 

dissolved inorganic nitrogen in the euphotic zone between 

study periods was hampered by the change in reporting limits 

and number of reported non-detected values in the 2004–06 

study. In the 1991–92 and 2004–06 studies, a significant 

difference existed between euphotic zone and hypolimnetic 

concentrations at all five stations, but particularly at the three 

deep stations. As previously discussed, a robust comparison 

was difficult for all nitrogen fractions between the two studies 

because of differences in method reporting limits.

Dissolved ammonia, nitrite, and nitrate were not detected 

in any of the blank samples submitted during the 2004–06 

study; therefore, decontamination procedures were deemed 

adequate to remove these analytes from sampling equipment. 

Mean relative standard deviations were 8 percent for dissolved 

ammonia and 1 percent for dissolved nitrite plus nitrate, 

based on replicate sample data collected during the 2004–06 

study. As with total phosphorus, most high relative standard 

deviations were for samples with low concentrations. Seventyone percent of ammonia analyses and 50 percent of nitrite plus 

nitrate analyses in replicate samples matched corresponding 

routine samples.

Limiting Nutrient

The limiting nutrient concept states that the ultimate 

yield of a crop will be limited by the essential nutrient most 

scarce relative to the specific needs of the crop (Ryding and 

Rast, 1989). This concept, in concert with the stoichiometry of 

the photosynthesis equation, has led to the widespread use of 

nitrogen-to-phosphorus ratios (N:P). These ratios commonly 

are used in eutrophication studies to evaluate if nitrogen or 

phosphorus was the nutrient most likely to limit phytoplankton 

growth. The atomic ratio of nitrogen to phosphorus, 16N:1P, 

in the photosynthesis equation corresponds to a mass ratio 

of 7.2N:1P. Typically, N:P values are calculated using the 

biologically available form of these two nutrients, dissolved 

inorganic nitrogen and dissolved orthophosphate. If N:P 

(by weight) is less than 7.2, then nitrogen may be limiting, 

whereas if N:P exceeds 7.2, then phosphorus may be limiting 

(Ryding and Rast, 1989).

The mean euphotic zone values of N:P for Coeur d’Alene 

Lake previously published for the 1991–92 study (Woods and 

Beckwith, 1997) were 34.4 for 1991 and 22.7 for 1992 and 

indicated a strong tendency towards phosphorus limitation 

of phytoplankton growth. The lower value for 1992 was a 

consequence of lower concentrations of dissolved inorganic 

nitrogen because dissolved orthophosphate concentrations 

were comparable during both years.

The calculation of N:P for 2004–06 dissolved inorganic 

nitrogen data was complicated by a reporting limit of 6 μg/L 

for dissolved orthophosphate and median concentrations of 

dissolved inorganic nitrogen less than 26 μg/L for 2 years in 

the study. These complications resulted in few samples with 

dissolved orthophosphate and dissolved inorganic nitrogen 

greater than their respective reporting limits. Values of both 

constituents for the calculation of N:P ratios were detected 

in only 36 percent of samples collected during the 1991–92 

study and 19 percent of samples collected during the 2004–06 

study. However, for a general comparison between study 

periods, the median N:P ratio values for each station when 

re 06

0

20

40

60

80

100

120

1991-922004-061991-922004-061991-922004-061991-92

2004-06

1991-922004-06

DISSOLVED INORGANIC NITROGEN 

CONCENTRATION, IN MICROGRAMS

PER LITER

Station 1 Station 3 Station 4 Station 5 Station 6

< 26< 26< 26< 26< 26

PELAGIC STATIONS AND YEARS

Euphotic zone

Hypolimnion

Figure 6. Median concentrations of dissolved 

inorganic nitrogen in the euphotic zone and hypolimnion 

at five pelagic stations, Coeur d’Alene Lake, Idaho, 

calendar years 1991–92 and water years 2004–06.
22 Coeur d’Alene Lake, Idaho: Insights Gained From Limnological Studies of 1991–92 and 2004–06

dissolved orthophosphorus and dissolved inorganic nitrogen 

were detected were calculated and compared. Median detected 

N:P ratios in the 1991–92 study ranged from 16 (station 6) 

to 26 (station 5). Median detected N:P ratios in the 2004–06 

study ranged from 7 (station 6) to 13 (station 3). Whereas 

the lake was clearly phosphorus-limited during 1991–92, the 

lake may have been much closer to the boundary value of 7.2 

that separates nitrogen from phosphorus limitation during 

2004–06. However, the data are insufficient to draw reliable 

conclusions regarding limiting nutrients.

Chlorophyll-a

Chlorophyll-a is the primary photosynthetic pigment 

of phytoplankton and, as such, is used as an estimator of 

phytoplankton biomass and an indicator of lake productivity. 

As discussed previously, the comparison of chlorophyll-a

concentrations between the two studies must recognize that 

different analytical methods were used. Concentrations 

of chlorophyll-a from samples collected in 1991-92 were 

adjusted using the NWQL regression equation to estimate the 

results that would have been expected using the fluorometric 

method that was applied in 2004-06. Adjusted concentrations 

from 1991–92 were used in statistical comparisons among 

stations and study periods.

Adjusted chlorophyll-a concentrations in Coeur d’Alene 

Lake during 1991–92 ranged from less than 0.1 to 3.1 μg/L; 

the highest concentrations were measured at stations 5 and 

6 in both years (Woods and Beckwith, 1997; appendix A). 

Chlorophyll-a concentrations during 2004–06 (analyzed 

fluorometrically) ranged from less than 0.1 to 17.9 μg/L; 

the highest concentrations were measured at station 6 

(appendix B). However, differences in median concentrations 

among stations were not statistically significant, and therefore, 

no spatial pattern was detected.

Median concentrations of chlorophyll-a within the 

euphotic zone of the five stations are plotted for each year 

in figure 7. Median concentrations increased significantly at 

all stations in the 2004–06 study compared to the 1991–92 

study. Adjusted median concentrations for 1991–92 ranged 

from 0.9 μg/L (stations 1, 3, and 4) to 1.2 μg/L (station 6). For 

2004–06, median concentrations ranged from 1.5 μg/L (station 

5) to 2.7 μg/L (station 6). For comparison, the unadjusted 

median values for the 1991–92 study also are plotted on 

figure 7. Although adjusted chlorophyll-a concentrations 

for the 1991–92 study increased compared to the unadjusted 

concentrations, they were still significantly less than 

concentrations during 2004–06 at every station.

Blank samples were not analyzed for chlorophyll-a

during the 2004–06 study. One replicate sample was analyzed 

for chlorophyll-a; relative standard deviation was 5 percent in 

comparison with the corresponding routine sample.

Trophic State

A nutrient load study conducted in 1975 as part of the 

National Eutrophication Survey led to the determination 

that Coeur d’Alene Lake was mesotrophic, or moderately 

productive (U.S. Environmental Protection Agency, 1977), 

which prompted continued observation of the lake trophic 

status. The 1991–92 study determined that the lake had 

become oligotrophic, or less productive, in terms of lake-wide 

mean chlorophyll-a and total phosphorus concentrations and 

mesotrophic in terms of Secchi-disc transparency depth, likely 

due to the documented reduction in nutrient loads throughout 

the basin from 1975 to 1991 (Woods and Beckwith, 1997). 

Although lake-wide mean chlorophyll-a and total phosphorus 

concentrations during the 2004–06 study have increased, the 

trophic status classification remained the same as determined 

by the 1991–92 study based on these variables. Lake-wide 

median values for the three limnological variables used to 

classify the trophic status are presented for both studies and 

compared to trophic classification data from Wetzel (1983) 

in table 7. Wetzel (1983) classifies a lake as oligotrophic if 

average or median total phosphorus concentrations are in 

the range of 3.0–17.7 μg/L, average or median chlorophyll-a

concentrations are in the range of 0.3–4.5 μg/L, and average 

or median Secchi-disc transparency depths are in the range 

of 5.4–28.3 m. Because the lake-wide median Secchi-disc 

transparency depth for Coeur d’Alene Lake (4.6 m) was less 

than this range, the lake is classified as mesotrophic based on 

this variable. The mesotrophic classification range for median 

Secchi-disc transparency depth is 1.5-8.1 m. Wetzel (1983) 

provides detailed discussion of the boundaries that separate 

trophic classifications.

1991-92

0

1

2

3

2004-061991-922004-061991-92

2004-06

1991-92

2004-06

1991-92

2004-06

PELAGIC STATIONS AND YEARS

CHLOROPHYLL-a CONCENTRATION, 

IN MICROGRAMS PER LITER

Chlorophyll-a, unadjusted

Chlorophyll-a

Station 1 Station 3 Station 4 Station 5 Station 6

Figure 7. Median concentrations of chlorophyll-a in the 

euphotic zone at five pelagic stations, Coeur d’Alene Lake, 

Idaho, calendar years 1991–92 and water years 2004–06.
Comparison of Limnological Conditions 23

Trace Metals

The comparison of trace metal concentrations between 

the two studies was restricted to total concentrations because 

dissolved concentrations were not analyzed in the 1991–92 

study. Of the 126 samples collected from the euphotic zone 

and hypolimnion during the 1991–92 study, median totalrecoverable concentrations were less than 1, 3.3, and 98.6 

μg/L, respectively, for cadmium, lead, and zinc (Woods and 

Beckwith, 1997). About 93 percent of cadmium, 24 percent of 

lead, and 13 percent of zinc concentrations were less than their 

analytical reporting limits of 1, 1, and 10 μg/L, respectively 

(table 6). Most trace-metal concentrations from station 6 were 

reported as “less-than” or censored data.

Zinc concentrations were the focus of a comparison of 

median concentrations in euphotic zone and hypolimnion 

samples from the five stations during the two studies (fig. 8). 

Concentrations in 2004–06 significantly decreased from 

those measured during 1991–92 for the euphotic zone and 

hypolimnion and at all stations except station 6. At every 

pelagic station except station 6, paired zinc concentrations 

were significantly higher in the hypolimnion than in the 

euphotic zone. During 1991–92, median zinc concentrations 

ranged from less than 10 (station 6) to 100 μg/L (station 4) in 

the euphotic zone and from less than 10 (station 6) to 132 μg/L 

(station 4) in the hypolimnion. During 2004–06, median zinc 

concentrations ranged from 2 (station 6) to 55 μg/L (station 4) 

in the euphotic zone and from 2 (station 6) to 78 μg/L (station 

4) in the hypolimnion.

A distinct spatial difference in total zinc concentrations 

is evident as shown in figure 8. The lowest median values 

are from station 6 which was far from the influence of the 

trace-metal-rich inflow of the Coeur d’Alene River. Although 

station 5 also would appear to be out of the influence of the 

Coeur d’Alene River, total zinc concentrations shown in 

figure 8 indicate otherwise. The three deep stations are directly 

influenced by the inflow plume of the Coeur d’Alene River 

and exhibited significantly higher total zinc concentrations 

than the two shallower stations. Concentrations at station 4 are 

slightly but statistically higher than all other stations.

At all pelagic stations except station 6, total cadmium 

and total lead concentrations decreased significantly from 

1991–92 to 2004–06. However, as stated previously, robust 

temporal comparisons for cadmium and lead are hampered by 

a substantial decrease in reporting limit in the 2004–06 study. 

Median cadmium and lead concentrations were significantly 

higher in the hypolimnion than in the euphotic zone at every 

station except station 6, where no significant stratification 

was detected regarding cadmium. As with zinc, the three deep 

stations exhibited significantly higher total cadmium and total 

lead concentrations than the two shallow stations; the highest 

total cadmium and total lead concentrations were measured at 

station 4.

Total cadmium was not detected in any of the blank 

samples submitted during the 2004–06 study; however, 

total lead and total zinc were detected in 24 and 19 percent, 

respectively, of the blank samples. Field notes recorded during 

one of the total lead and total zinc detections (April 2005) 

state that pieces of a rubber seal in the grab sampling device 

were in the blank sample water during sample processing. 

The sampling device was soon replaced. Trace metals 

concentrations in samples collected around this time may be 

biased high. Mean relative standard deviations in replicate 

sample data were 2 percent for total cadmium, 3 percent for 

total lead, and 5 percent for total zinc. Therefore, variability 

induced during sample processing and analysis was low for 

these constituents.

Table 7. Trophic state based on lake-wide median values for three limnological variables, Coeur d’Alene, Idaho, calendar years 

1991–92 and water years 2004–06.

[TS classification source: Wetzel, 1983. Abbreviations: μg/L, microgram per liter; m, meter; TS, trophic state; O, oligotrophic; M, mesotrophic]

Study

Total phosphorus (μg/L) Chlorophyll-a (μg/L) Secchi-disc transparency depth (m)

Median TS

TS 

classification 

range for 

median

Median TS

TS 

classification 

range for 

median

Median TS 

TS 

classification 

range for 

median

1991–92 5.0 O 3.0–17.7 0.5 O 0.3–4.5 4.4 M 1.5–8.1

2004–06 7.0 O 3.0–17.7 1.7 O 0.3–4.5 4.6 M 1.5–8.1
24 Coeur d’Alene Lake, Idaho: Insights Gained From Limnological Studies of 1991–92 and 2004–06

Pelagic and Littoral Water Quality

The 1991-92 study included two littoral sampling events 

and the 2004-06 study included eight sampling events. To 

compare pelagic and littoral water quality between the two 

studies, only samples collected during the same weeks were 

compared. For pelagic and littoral comparisons, the latter 

study period is termed “2004–05” because comparison data 

were not collected during the same weeks in water year 2006. 

Mutual constituents sampled between littoral and pelagic 

stations during the two studies included total phosphorus, 

chlorophyll-a, and zinc. Comparisons were made using two 

methods:

• Constituent concentrations at the pelagic euphotic zone 

and littoral stations were compared as a whole for 

common sampling weeks in September 1991, August 

1992, August 2004, and July 2005. Both “NS” and 

“S” littoral stations were included in the comparison; 

however, total zinc was the only constituent sampled 

and evaluated at the “S” stations. Data were compared 

using the Mann-Whitney hypothesis test because all 

data during these periods were reported greater than 

the reporting limit. Concentrations were compared 

by station type (pelagic or littoral) and between study 

periods by station type.

• Constituent concentrations at each pelagic station 

(euphotic zone) and at the corresponding closest littoral 

stations for the common sampling weeks were paired 

and tested using the Wilcoxon Signed-Ranks test. For 

example, constituent concentrations at pelagic station 

1 are compared with concentrations at three nearby 

littoral stations, NS10, NS11, and NS12. Paired littoral 

stations were selected based on spatial proximity to the 

pelagic station and based on hydrologic knowledge of 

the area. “NS” and “S” littoral stations were included 

in the comparison; however, total zinc was the only 

constituent sampled and evaluated at the “S” stations. 

All comparison data were reported greater than the 

reporting limit.

Comparison 1 indicated that when data sets were 

compared as a whole, median total phosphorus concentrations 

were significantly lower in the littoral zone than in the pelagic 

euphotic zone for weeks sampled in 2004–05. Median total 

zinc concentrations were significantly lower in the littoral 

zone than in the pelagic euphotic zone for weeks sampled in 

1991–92. In all other cases, total phosphorus, chlorophyll-a, 

and total zinc concentrations were statistically similar for dates 

sampled in both study periods. Zinc concentrations for the 

littoral zone and pelagic euphotic zone in the 2004–05 study 

decreased significantly from the 1991–92 study.

Comparison 2 indicated that total phosphorus, 

chlorophyll-a, and total zinc concentrations are statistically 

similar between the pelagic stations and their closest littoral 

stations on the same weeks sampled. Table 8 presents the 

median values and ranges for each constituent for each 

pelagic station and its closest paired littoral stations. A true 

comparison at station 6 could be made only for total zinc 

concentrations because chlorophyll-a and total phosphorus 

were not collected at any of the closest littoral stations. 

However, chlorophyll-a and total phosphorus concentrations 

were significantly higher and total zinc concentrations were 

significantly lower at station 6 than at NS1 (near station 5), 

the closest littoral station where all three constituents were 

collected. This observation along with observations previously 

stated in this report regarding concentration gradients for 

nutrients and metals, indicate that water-quality conditions 

at station 5 (and corresponding littoral stations) are slightly 

different than at station 6.

Because statistically significant differences were 

determined in some analyte concentrations among pelagic 

stations, comparison 2 provides a more valid determination 

than comparison 1 of the difference between littoral and 

pelagic water quality because use of this method pairs each 

pelagic station with the respective littoral area. Additionally, 

any error introduced by temporal variation was decreased 

because pelagic samples were compared only with littoral 

samples collected during the same week.

Physical Limnological Processes

Focused limnological studies of Coeur d’Alene Lake 

were conducted between the 1991–92 and 2004–06 studies 

and included many variables that were sampled in the 1991–92 

and 2004–06 studies. These post-1992 studies benefited the 

design of the 2004–06 study and added spatial and temporal 

information for many variables. The limnological basis 

for sampling the lake during the 2004–06 study (table 2) 

recognized the important role played by physical limnological 

processes in determining how the lake may be affected in the 

future by watershed-remediation activities associated with the 

Bunker Hill Superfund Site OU3 ROD and Lake Management 

Plan.

Figure 8. Median concentrations of total zinc in 

euphotic zone and hypolimnion at five pelagic stations, 

Coeur d’Alene Lake, Idaho, calendar years 1991–92 and 

water years 2004–06.

08

0

40

80

120

160

1991-92

2004-06

1991-922004-061991-92

2004-061991-922004-061991-92

2004-06

PELAGIC STATIONS AND YEARS

TOTAL ZINC CONCENTRATION, 

IN MICROGRAMS PER LITER

Station 1 Station 3 Station 4 Station 5 Station 6 <10 <10

Euphotic zone

Hypolimnion
Comparison of Limnological Conditions 25

Two recent reports (URS Greiner, Inc., and CH2M-Hill, 

Inc., 2001 and Woods, 2004), noted the importance of physical 

limnological processes in the fate and transport of constituents 

and, by extension, water-quality conditions in Coeur d’Alene 

Lake. Those processes include, but are not limited to, lake 

hydraulic residence time, wind-generated circulation, and 

in-lake routing of inflow plumes.

Hydraulic Residence Time

Surface-water runoff from a drainage basin commonly 

is the primary source of inflow to most lakes; ground-water 

inflow and direct precipitation on the lake surface usually are 

of much smaller magnitude. The rate at which water enters 

and leaves a lake affects the amount of turbulence within 

the lake water column, both in the horizontal and vertical 

dimensions. Limnologists have long used the ratio of inflow 

rate to lake volume, commonly termed flushing rate (Ryding 

and Rast, 1989), to quantify this physical limnological 

process. As flushing rate increases, the hydrologic influence 

on the lake from the drainage basin also increases because the 

lake volume is frequently replaced. The inverse of flushing 

rate is retention time, which represents the time theoretically 

needed to fill a lake if the lake were empty. If lake volume 

is divided by lake outflow rate instead of inflow rate, then 

the time needed to empty the lake, the hydraulic residence 

Table 8. Comparisons of medians and ranges of total phosphorus, chlorophyll-a, and total zinc 

concentrations at pelagic and paired littoral stations on common weeks sampled, Coeur d’Alene Lake, Idaho, 

water years 2004–05.

[Abbreviations: μg/L, microgram per liter; <, less than; –, not analyzed]

Stations

Total phosphorus 

concentration (μg/L)

Chlorophyll-a concentration 

(μg/L)

Total zinc concentration 

(μg/L)

Median Range Median Range Median Range

Station 1

Pelagic station 1 6 2–11 1.7 0.4 –2.7 55 34–65

Littoral station NS10 5 3–14 1.7 0.58–3.5 52 34–98

Littoral station NS11 7.5 3–15 1.2 0.61–2.0 48 34–97

Littoral station NS12 5 3–8 1.2 0.83–3.4 52 31–83

Station 3

Pelagic station 3 6 2–10 1.4 <0.1–2.8 54 36–75

Littoral station NS6 4.5 3–23 1.4 0.38–2.1 58 36–77

Littoral station NS7 4 3–13 1.4 0.39–2.1 66 43–100

Littoral station NS8 5.5 5–14 1.4 0.4 –2.1 52 32–106

Littoral station NS9 4.5 3–14 1.1 0.78–1.6 55 39–86

Station 4

Pelagic station 4 5 3–12 1.5 0.2–2.4 54 42–82

Littoral station NS3 6.5 5–15 1.2 0.45–2.1 55 37–94

Littoral station NS4 6 4–12 1.0 0.86–2.6 56 36–83

Littoral station NS5 5 3–16 1.2 0.59–2.3 54 38–74

Station 5

Pelagic station 5 10 7–31 1.4 0.7–2.7 36 3–61

Littoral station NS1 11.5 7–27 1.2 0.33–4.8 19 6–90

Littoral station NS2 7 5–15 1.2 0.46–3.5 44 13–77

Station 6

Pelagic station 6 17 10–36 2.9 0.5–5.6 2 1–4

Littoral station S5 – – – – 2 1–2

Littoral station S6 – – – – 2 2–2

Littoral station NS1 10 7–27 0.9 0.3–2.3 18 6–90
26 Coeur d’Alene Lake, Idaho: Insights Gained From Limnological Studies of 1991–92 and 2004–06

time, is obtained. On an annual basis, retention time and 

hydraulic residence time often are comparable. Hydraulic 

residence time was selected for analysis in this report because 

outflow rates for Coeur d’Alene Lake have been measured 

for many years; measurements of the sum of inflow rates 

for all significant inflow sources are rare for most lakes. 

Although retention time and hydraulic residence time are 

theoretical concepts, the processes that they incorporate are 

important for understanding fate and transport of constituents 

in lakes. In years of greater than normal inflow and outflow, 

increased water column turbulence and advective transport of 

constituents can be expected. Conversely, years of less than 

normal inflow and outflow produce less water column mixing 

and may increase the constituents trapped in the lake.

The hydraulic residence time for Coeur d’Alene Lake 

is 0.50 year based on a normal full-pool volume of 2.8 km3

divided by the mean annual outflow rate of 5.6 km3/yr. 

Outflow statistics for the lake were derived for a 93-year 

period of record (1913–2006) for the USGS gaging station on 

Spokane River near Post Falls, Idaho (U.S. Geological Survey, 

2007). During that period of record, however, annual mean 

outflow volume varied widely. For the minimum outflow 

rate of 1.9 km3/yr, the hydraulic residence time increased 

to 1.5 years; conversely, for the maximum outflow rate of 

10.5 km3/yr, hydraulic residence time decreased to 0.27 year. 

This range of hydraulic residence times and historical outflow 

rates indicate that the lake volume could be replaced in as few 

as 98 days or as many as 548 days. This range also represents 

an index of the physical limnological process of water column 

turbulence and the presumed relation with hydraulic residence 

time. Retention of constituents delivered from the drainage 

basin to Coeur d’Alene Lake is expected to decrease as 

hydraulic residence time decreases. In addition to inter-annual 

variability, outflow from the lake varies intra-annually in 

response to climate conditions in the drainage basin. During 

the 1913–2006 period of record, the smallest monthly mean 

outflow of 0.07 km3/mo was in August, whereas the largest 

monthly mean outflow of 1.3 km3/mo was in May. Based on 

these outflow rates, constituents inflowing to the lake are more 

likely to be retained in August when water column turbulence 

and water outflow are minimal.

Although insight was gained into the relation of inflow 

or outflow magnitude on the generation of turbulence and 

advective transport within lakes, the concepts of retention and 

hydraulic residence times remain theoretical because lakes 

rarely are filled or emptied. The two concepts are best suited 

for general comparisons among lakes representing wide ranges 

of retention and hydraulic residence times.

Wind-Generated Circulation

The physical, chemical, and biological responses of a lake 

to the delivery of water and associated constituents from the 

drainage basin are closely tied to shape, exposure to wind, and 

depth of the lake. A long, narrow lake shape, like that of Coeur 

d’Alene Lake, is more prone to channelized flow along its 

major axis. Shape and surface area of a lake are determinants 

of wind exposure. Increased wind exposure enhances the 

development of large-scale turbulent processes such as surface 

waves and internal seiches, which can displace large masses 

of water in the horizontal and vertical dimensions, important 

mechanisms for water column mixing. Deep lakes, such as 

Coeur d’Alene Lake, are less prone to turbulent, full-depth 

mixing by wind energy, so lakebed sediments are less likely 

to be periodically re-suspended except perhaps by internal 

waves near the thermocline. The low frequency of turbulent, 

full-depth mixing in deep lakes also restricts the exchange of 

dissolved, colloidal, and particulate constituents between the 

upper and lower water columns.

Routing of Inflow Plumes

The movement of riverine inflows within a lake can be 

quite complex because of lake characteristics such as shape, 

depth, and temporal and spatial differences in density between 

riverine and lake water. Overflow, interflow, and underflow 

are three generalized methods of inflow plume routing 

(Fischer and others, 1979). Overflow occurs if the inflow 

plume is warmer (less dense) than the lake; river water floats 

on the lake surface. Interflow occurs when the inflow plume 

is colder than the lake upper water column but is warmer than 

the lower water column; interflow is routed to the lake depth 

where the temperature, or density, of the inflow plume and 

lake are equal. Underflow occurs when the inflow plume is 

colder than, or near the temperature of, the lake lower water 

column. Turbulence at the interface of the inflow plume and 

the lake mixes the two water masses until thermal equilibrium 

is reached. The spatial extent of inflow plume routing is 

highly dependent on the magnitude of riverine discharge. 

Riverine inflows generated by snowmelt runoff and floods 

can penetrate farther into the receiving lake because the large 

inflow volumes produced by such events increase advective 

transport.

The fate and transport of constituents such as nutrients, 

trace metals, and sediment within and occasionally through 

Coeur d’Alene Lake are highly dependent on inflow plume 

routing of the two primary inflow sources, the Coeur d’Alene 
Comparison of Limnological Conditions 27

and St. Joe Rivers. Inflow plume routing was evaluated using 

data from the 1991–92 and 2004–06 limnological studies as 

well as data from several other studies of the lake. For the 

1991–92 study, available data included water temperatures 

for the two rivers (Harenberg and others, 1992; 1993) and 

numerous full-depth profiles of water temperatures conducted 

for most months at pelagic stations (Woods and Beckwith, 

1997). An inflow plume routing evaluation also was evaluated 

for water year 1999 using similar water-temperature data; 

however, pelagic water column profiles were conducted only 

during June through October at pelagic stations 1, 3, 4, and 5 

(URS Greiner, Inc., and CH2M Hill, Inc., 2001).

Forty-four comparisons of inflow and lake temperatures 

reported for 1991–92 and 1999 (URS Greiner, Inc., and 

CH2M Hill, Inc., 2001) indicated that overflow was the most 

common mode of inflow plume routing, occurring in about 

60 percent of the comparisons (URS Greiner, Inc., and CH2M 

Hill, Inc., 2001). Interflow or underflow each occurred in 

about 20 percent of the comparisons. Overflow occurred in 

all months except October, November, and December; during 

those 3 months, underflow was the most likely mode of inflow 

plume routing. Interflow tended to occur during spring or 

autumn when the lake was likely transitioning into or out 

of thermal stratification. Inflow volume also was evaluated 

as part of the 44 comparisons because of its affect on the 

spatial extent of inflow plume routing. At small inflows, the 

influence of the plume on the lake was diminished by rapid 

mixing and equilibration of riverine and lake temperatures; 

the opposite was true for large inflows. Underflows tended 

to be associated only with small inflows, typical for October 

through December. Underflows occurred during that 3-month 

period because the Coeur d’Alene and St. Joe Rivers cooled 

more rapidly than the lake, which has a much greater capacity 

to store and retain heat captured during the summer months. 

Overflows occurred over a wide range of inflows because 

the Coeur d’Alene and St. Joe Rivers each have lengthy 

backwater-affected reaches that capture a large amount of 

solar radiation.

During June 1999, USGS scientists using specialized 

water-quality instrumentation and water column 

sampling methods tracked discharge and chemistry of the 

Coeur d’Alene and St. Joe River inflow plumes into and 

through Coeur d’Alene Lake. The short-term study sought to 

answer two questions: (1) Can riverine inflows and associated 

chemical nature be clearly identified within the lake? (2) 

Do sediments, nutrients, and trace metals carried by riverine 

inflows travel far enough into the lake to be discharged out 

of the lake into the Spokane River? The field work was 

conducted during June 2–3, 1999, at pelagic stations 1–5 in 

addition to three stations at the mouths of the Coeur d’Alene 

and St. Joe Rivers and at the lake outlet to the Spokane 

River. Study results clearly identified the riverine inflows as 

a combination of overflow and interflow within the upper 

5–13 m of the lake, from station 4 and northward to the lake 

outlet (URS Greiner, Inc., and CH2M Hill, Inc., 2001). Much 

of the lake south of station 4 is shallow enough to allow fulldepth mixing of the two riverine inflows. Light transmission, 

conductivity, and concentrations of lead, zinc, and nitrogen 

differed substantially between the riverine inflows and lake 

water. Lead concentrations delivered by the Coeur d’Alene 

River were higher than concentrations in lake water. Zinc 

concentrations, delivered almost exclusively by the Coeur 

d’Alene River, were lower than concentrations in lake water. 

Light transmission, conductivity, and nitrogen concentrations 

in riverine water also were lower than concentrations in lake 

water. The chemical nature of water exiting the lake to the 

Spokane River during the June 1999 experiment was more 

closely related to riverine inflows than to lake water; however, 

this is not expected to be true throughout the year.

Numerous riverine inflow temperatures and water column 

profiles of water temperature were available for water years 

2004 and 2005 during the 2004–06 study to evaluate inflow 

plume routing. Table 9 lists 15 riverine inflow temperatures 

measured within two weeks of a limnological sampling trip 

in water years 2004 and 2005, similar to a table presented 

in URS Greiner, Inc., and CH2M Hill, Inc. (2001). One 

measurement is shown for which there was no sampling 

data. The water temperatures and discharges of the Coeur 

d’Alene and St. Joe Rivers were compared to the range of 

water column temperatures at pelagic station 3, the deepest 

area in the lake. Of the 15 comparisons, 7 indicated overflow, 

6 indicated interflow, and 2 indicated underflow (table 9). 

Underflows occurred in December of both years because 

inflowing rivers cooled faster than the lake, which had a much 

larger heat storage capacity. Interflows occurred in early April, 

May, and June and in early September 2004 and in late March 

and mid-May 2005. The predominance of interflows during 

spring months was partly due to more rapid warming of the 

inflowing rivers than the lake, which was emerging from 

winter cooling. Overflows were recorded during October of 

both years, as late summer heating kept riverine temperatures 

similar to lake temperatures. For summer months, overflow 

was recorded only in July 2004 and during June, July, and 

August 2005. Cold (2.0–2.3°C) riverine water that entered the 

lake in February 2005 during a period of inverse stratification 

(lake water at 3.4°C with maximum density, underlying colder, 

less dense water) caused an overflow condition.
28 Coeur d’Alene Lake, Idaho: Insights Gained From Limnological Studies of 1991–92 and 2004–06

Benthic Flux

The primary focus of the 1991–92 study was on nutrients 

and lake productivity; collection of trace metal samples from 

the lake water column was less frequent and at fewer depths. 

However, lakebed sediments also were sampled during this 

period for characterization of concentration, partitioning, and 

environmental availability of selected trace metals (Horowitz 

and others, 1993; 1995a; 1995b; 2001). These additional 

sediment studies estimated that 75 million metric tons of 

metals-enriched sediments cover about 85 percent of the 

bottom of Coeur d’Alene Lake. These sediments range in 

thickness from 17 to more than 119 cm. Horowitz and others 

(1993) reported mean concentrations of arsenic (151 mg/kg), 

cadmium (62 mg/kg), lead (1,900 mg/kg), mercury (1.8 

mg/kg), and zinc (3,600 mg/kg) in lakebed surface sediments 

in Coeur d’Alene Lake. Naturally occurring background 

concentrations in lakebed sediments were reported for arsenic 

(5 mg/kg), cadmium (3 mg/kg), lead (24 mg/kg), mercury 

(0.05 mg/kg), and zinc (110 mg/kg) (Horowitz and others, 

1993). Metals-enriched sediments in Coeur d’Alene Lake 

generally are extremely fine-grained and are susceptible to 

remobilization by river- and wind-induced lake currents.

Although eutrophication by nutrients and contamination 

of lakebed sediments by trace metals may have appeared 

to be unrelated water-quality problems for Coeur d’Alene 

Lake, the potential development of water column anoxia 

near the lakebed could release nutrients and trace metals 

from lakebed sediments into the overlying water column. 

When anoxia develops, a well-known consequence of 

eutrophication, reductive dissolution of metal oxides, such 

as iron and manganese, can occur in lakebed sediments and 

the hypolimnion (Brezonik, 1994). At dissolved-oxygen 

concentrations less than 1 mg/L, iron-phosphate complexes 

may become unstable and dissolve and release phosphorus 

from lakebed sediments into the hypolimnion (Jones and 

Bowser, 1978; Baccini, 1985). Horowitz and others (1993) 

reported that most lakebed trace metals in Coeur d’Alene Lake 

were associated with iron oxides. Under anoxia, the reductive 

dissolution of iron oxides could release trace metals into the 

Table 9. Inflow plume routing based on comparison of riverine inflow temperatures and water column temperature ranges at pelagic 

station 3, Coeur d’Alene Lake, Idaho, water years 2004–05.

[Station locations are shown in figure 1. St. Joe River (USGS gaging station 12415140); Coeur d’Alene River (USGS gaging station 12413860). Abbreviations:

°C, degrees Celsius; m3/s, cubic meter per second; USGS, U.S. Geological Survey; –, not analyzed]

Date of 

river 

sampling

St. Joe River Coeur d’Alene River Pelagic station 3 Inflow plume routing

Water 

temperature

(°C)

Instantaneous 

discharge

(m3

/s)

Water 

temperature

(°C)

Instantaneous 

discharge

(m3/s)

Date 

of lake 

sampling 

Water 

temperature 

range

(°C)

Overflow Interflow Underflow

Water year 2004

10-08 14.9 11.9 14.4 12.5 10-22 6.6 –14.0 X

12-08 1.6 42.5 3.6 53.8 12-03 6.6 – 6.6 X

04-06 6.5 195 6.8 210 04-14 4.2 – 9.3 X

05-08 8.3 195 9.4 108 05-18 4.9 –12.9 X

06-08 10.8 139 11.8 87.8 06-22 5.7 –18.1 X

07-19 21.8 34.0 22.9 22.1 07-20 5.9 –22.6 X

09-01 17.4 14.2 17.3 4.39 08-25 6.1 –21.1 X

Water year 2005

10-12 12.9 15.6 13.4 18.7 10-20 6.5 –13.7 X

12-13 3.0 180 3.3 312 12-04 6.7 – 7.4 X

02-07 2.0 79.3 2.3 79.3 01-25 3.4 – 2.4 X

03-14 6.0 51.0 7.2 34.0 – – 

03-30 3.3 227 3.5 232 04-07 4.2 – 4.5 X

05-12 8.3 178 11.3 73.6 05-24 5.2 –12.5 X

06-27 19.1 42.5 18.8 21.0 06-14 5.2 –14.6 X

07-18 20.3 18.7 22.4 16.1 07-20 5.5 –21.3 X

08-25 20.8 7.65 21.0 3.96 09-01 5.7 –19.9 X
Comparison of Limnological Conditions 29

water column of the lake. The potential development of anoxia 

in Coeur d’Alene Lake prompted a study by the USGS in 

1987. Hypolimnetic dissolved oxygen concentrations as low as 

4 mg/L were detected during late summer in the deep northern 

basin of the lake (Woods, 1989).

Based on published literature related to anoxic releases 

of constituents from lakebed sediments, the 1991–92 study 

did not anticipate releases of nutrients and trace metals 

from the lakebed sediments because hypolimnetic dissolved 

oxygen concentrations exceeded 1 mg/L. The study’s focus 

was oriented toward understanding the lake assimilative 

capacity for nutrients to maintain adequate concentrations of 

hypolimnetic dissolved oxygen. However, additional studies 

done in Coeur d’Alene Lake by N.S. Simon (U.S. Geological 

Survey, written commun., 1993), Kuwabara and others (2000; 

2003; 2006), and Winowiecki (2002) after the 1991–92 study 

detected the presence of a benthic flux, the movement of 

constituents into and out of lakebed sediments, even in the 

presence of hypolimnetic dissolved oxygen concentrations 

greater than 1 mg/L.

Benthic fluxes define the transport of dissolved 

constituents across the sediment-water interface. In the 

absence of advection, this transport primarily is a function 

of concentrations in the overlying water and in porewater 

just below the interface (the chemical gradient) and the 

molecular or eddy diffusion coefficients for the constituents 

of interest. Benthic fluxes have both direction and magnitude. 

The direction indicates whether the sediment supplies or 

removes dissolved constituents to or from the overlying 

water. Sediments act as a source when dissolved-constituent 

concentrations in the porewater are greater than in the 

overlying water (positive flux) or a sink when dissolvedconstituent concentrations in the overlying water are greater 

than in the porewater (negative flux). The magnitude of 

benthic fluxes depends on the steepness of the chemical 

gradient and the transport mechanism (molecular compared 

to eddy diffusion); the magnitude can be used to determine 

the relative importance of sediments as a source or sink for 

dissolved constituents in a lake.

Balistrieri (1998) evaluated the benthic flux studies 

of N.S. Simon (U.S. Geological Survey, written commun., 

1993) and Winowiecki (2002) conducted in September 1992. 

Constituent concentrations in water overlying sediments and 

in porewater were used by Balistrieri (1998) to calculated 

benthic fluxes using Fick’s First Law, which assumes that 

benthic fluxes were controlled by molecular diffusion across 

the sediment-water interface. Porewater was collected by N.S. 

Simon (U.S. Geological Survey, written commun., 1993) and 

Winowiecki (2002) using diffusion-controlled equilibrator 

samplers, also known as peepers or dialyzers, which were 

inserted into the lakebed sediments by divers. Balistrieri 

(1998) noted that oxidation of the porewater samples likely 

occurred during collection and handling of the samples. This 

oxidation probably affected the concentrations of certain 

metals in the porewater (iron and metals that adsorb to 

iron-oxide phases), and thereby, influenced the benthic flux 

calculations.

The benthic flux study of Coeur d’Alene Lake conducted 

in August 1999 and discussed by Kuwabara and others (2000) 

used an in situ benthic flux chamber that isolated a volume 

of water overlying the sediment and periodically sampled 

constituent concentrations in the chamber. Fluxes were 

calculated as a function of time on the basis of changes in 

dissolved-constituent concentrations during deployment of the 

chamber. Using this method, no assumption is required about 

the mechanism of transport (molecular or eddy diffusion) to 

determine fluxes.

The results of benthic flux measurements from the 

chamber method are summarized in table 10 for dissolved 

cadmium, iron, lead, manganese, and zinc. Each value is 

reported as micrograms per square centimeter of lakebed 

surface per year (μg/cm2

/yr) moving out of the lakebed 

sediments. The in situ benthic flux chamber method is 

considered more representative of conditions in Coeur d’Alene 

Lake, compared to the peeper method by Winowiecki (2002), 

because the in situ benthic flux chamber method trapped an 

existing parcel of lakebed sediment, associated porewater, 

and overlying lake water, and measured benthic flux without 

major alteration of pre-existing conditions. Dissolved oxygen 

concentrations in the lower hypolimnion of the lake near 

the experiment stations were consistently high, 8–10 mg/L, 

during August 1999, and oxygen consumption rates in 

the chamber measured during the experiment were small, 

6.0–9.5 millimoles of oxygen per square meter per day. Water 

in the chambers did not become anoxic at any point during the 

experiment (Kuwabara and others, 2000). Therefore, oxygen 

consumption in the chamber during the experiment did not 

substantially alter the chemical environment at the sedimentwater interface from ambient conditions.

Based on the in situ benthic flux chamber results listed 

in table 10, dissolved cadmium, iron, lead, manganese, and 

zinc had positive fluxes out of the lakebed sediments. The 

smallest flux was for lead, 1.9 μg/cm2

/yr; the largest was for 

manganese, 3,700 μg/cm2/yr. Standard error was high (greater 

than 50 percent) relative to average flux values reported for 

iron, lead. and manganese (Kuwabara and others, 2000).

The benthic flux of dissolved nutrients and DOC also 

were measured by the in situ benthic flux chamber method 

(table 11). The benthic fluxes for orthophosphate, nitrite 

plus nitrate, ammonia, the sum of nitrite plus nitrate and 

ammonia (dissolved inorganic nitrogen), and DOC were all 

positive, indicating movement out of the lakebed sediments. 
30 Coeur d’Alene Lake, Idaho: Insights Gained From Limnological Studies of 1991–92 and 2004–06

The smallest flux was for orthophosphate, 7.2 μg/cm2/yr; the 

largest was for DOC, 2,700 μg/cm2/yr. Kuwabara and others 

(2000) determined that molecular diffusion was likely the 

dominant transport mechanism for constituents across the 

sediment-water interface in Coeur d’Alene Lake.

The flux of dissolved constituents across the sedimentwater interface is a result of the coupling of physical, 

chemical, and biological processes (Santschi and others, 

1990). Biologically mediated chemical reactions can mobilize 

dissolved constituents from solid phases within the lakebed 

sediments, thereby allowing transport by molecular and 

eddy diffusion. Oxidation of organic matter in the upper 

sediments of aquatic environments can affect the partitioning 

of certain constituents between sediment and porewater and 

produces nutrients such as ammonia and orthophosphate 

that are needed for phytoplanktonic production. Studies of 

freshwater and marine sediments indicate that the oxidation 

of organic matter proceeds using a thermodynamically 

predictable sequence of oxidants: oxygen, nitrate, manganese 

oxyhydroxides, ferric oxyhydroxides, and sulfate (Froelich 

and others, 1979; Berner, 1980; Pedersen and Losher, 1988; 

and Luther and others, 1998). These reactions are reflected 

in the composition of porewater as a function of depth. With 

increasing depth, oxygen and nitrate disappear followed by 

the appearance of nitrite, ammonia, and dissolved manganese 

and iron, then sulfate disappears. Oxygen is the primary 

oxidant of organic matter in the oxic zone. Suboxic conditions 

occur when oxygen concentrations are very low and nitrate, 

manganese oxyhydroxides, and ferric oxyhydroxides are used 

as oxidants. The location of this zone in the upper sediments 

of Coeur d’Alene Lake is of particular interest with respect 

to metals because the reduction of manganese and ferric 

oxyhydroxides can result in the release of associated trace 

metals (cadmium, lead, and zinc) into the dissolved phase. 

The absence of oxygen and oxidation of organic matter by 

sulfate characterize anoxic conditions. Sulfate reduction 

results in the production of sulfide. This sulfide appears 

either in porewater or is precipitated as a metal sulfide phase, 

if there are sufficient concentrations of dissolved metals, 

primarily iron. The depth scale where these reactions occur 

can be large (meters) or small (millimeters to centimeters) 

depending on the supply of organic matter, bottom-water 

anoxia, and sedimentation rates. If these reactions are 

compressed into the upper few centimeters just below the 

sediment-water interface, then concentrations of oxygen, 

nitrate, and sulfate should be lower in porewater just below 

the interface, relative to concentrations in the overlying water 

because of organic matter diagenesis. Thus, the direction of 

Table 10. Benthic flux of dissolved metals measured by an in-situ flux chamber, Coeur d’Alene Lake, Idaho, 1999.

[Station locations are shown in figure 1. Latitude, longitude in degrees, minutes, seconds, North American Datum of 1927 (Kuwabara and 

others, 2000). Benthic flux: average flux values were determined for multiple samplings of flux chambers at each site. Data from Kuwabara and 

others (2000). Values rounded to 2 significant figures. Abbreviations: μg/cm2/yr, microgram per square centimeter per year]

Station name Latitude, longitude

Benthic flux (μg/cm2

/yr)

Cadmium Iron Lead Manganese Zinc

Main channel, BF1 47°30'26", 116°51'27" 3.1 180 2.4 3,700 280

Mica Bay, BF2 47°36'02", 116°49'53" 2.3 110 1.9 3,000 350

Table 11. Benthic flux of nutrients and dissolved organic carbon measured by an in-situ flux chamber, Coeur d’Alene Lake, Idaho, 1999.

[Station locations are shown in figure 1. Latitude, longitude in degrees, minutes, seconds, North American Datum of 1927 (Kuwabara and others, 2000). 

Benthic flux: average flux values were determined for multiple samplings of flux chambers at each site. Data from Kuwabara and others (2000). Values rounded 

to 2 significant figures. Abbreviations: μg/cm2/yr, microgram per square centimeter per year]

Station 

name Latitude, longitude

Benthic flux, (μg/cm2

/yr)

Orthophosphate

Nitrite plus 

nitrate 

as nitrogen 

Ammonia as 

nitrogen 

Dissolved 

inorganic 

nitrogen

Dissolved 

organic 

carbon

Main channel, BF1 47°30'26", 116°51'27" 7.2 160 58 220 2,700

Mica Bay, BF2 47°36'02", 116°49'53" 22 210 110 320 1,800
Comparison of Limnological Conditions 31

benthic fluxes for these species (oxygen, nitrate, and sulfate) 

should be into the sediment. Porewater profiles of sulfate 

within the upper 30 cm of Coeur d’Alene Lake sediments 

indicate that the transition from oxic, through suboxic, to 

anoxic conditions exists, depending on location, either within 

the upper 1 cm or the upper 2–5 cm just below the interface 

(Balistrieri, 1998). Kuwabara and others (2000) measured 

oxygen benthic fluxes that ranged from -6.0 to -9.5 millimoles 

of oxygen per square meter per day, consistent with oxygen 

consumption by the sediments. Analytical methods employed 

by Kuwabara and others (2000) did not separate nitrate and 

nitrite concentrations, so no benthic fluxes were determined 

for nitrate alone.

In contrast, oxidation of organic matter produces nitrite, 

ammonia, orthophosphate, and dissolved manganese and 

iron. The concentrations of these constituents should be 

higher in porewater relative to the overlying water. Thus, the 

direction of benthic fluxes for these species should be out of 

the sediments if no other reactions (adsorption of phosphorus 

to iron oxides) trap them in the sediments. For example, when 

a thin oxic layer overlies a suboxic or anoxic layer, dissolved 

iron produced in the suboxic zone can diffuse into the oxic 

zone to be oxidized and precipitated as solid-phase iron 

oxyhydroxides. These iron oxides could then adsorb dissolved 

orthophosphate. This scenario would effectively trap iron 

and orthophosphate in the sediment and prevent them from 

diffusing into the overlying water. However, benthic flux data 

strongly indicate that sediments in Coeur d’Alene Lake act 

as a source of dissolved iron and orthophosphate, as well as 

ammonia and manganese, to the overlying water (tables 10

and 11). Overall, however, there is a net sedimentation of these 

constituents to lake sediments when they are associated with 

particulate material, as demonstrated in the lake mass balance 

calculations for metals (table 5).

Oxidation of organic matter can indirectly mobilize or 

sequester constituents such as cadmium, lead, and zinc. If 

these trace metals are predominantly supplied to the sediments 

in particulate form and in association with iron and manganese 

oxides, then the reduction of iron and manganese oxides 

during organic matter oxidation (after all available dissolved 

oxygen and nitrate are exhausted and reduced) results in the 

release of not only dissolved iron and manganese, but all 

other trace metals associated with those phases. The dissolved 

trace metals can be either transported by molecular or eddy 

diffusion across the sediment-water interface, or if sufficient 

concentrations of sulfide are present, be precipitated or 

co-precipitated as authigenic metal-sulfide phases. Although 

authigenic sulfides may be forming in Coeur d’Alene Lake, as 

reported by Harrington and others (1998), most benthic flux 

data indicate that sediments in Coeur d’Alene Lake act as a net 

source of dissolved cadmium, lead, and zinc to the overlying 

water (table 10).

The 2004–06 limnological study sought to increase 

understanding of benthic flux by identifying it as an important 

water-quality issue for Coeur d’Alene Lake through the studies 

by Horowitz and others (1993, 1995a, 1995b); Balistrieri 

(1998); Harrington and others (1998); Kuwabara and others 

(2000); and Woods (2004). The logistical difficulties involved 

in installation and retrieval of diffusion-controlled samplers or 

in situ flux chambers prompted the design of a boat deployed, 

modified gravity coring device that could retrieve undisturbed 

samples of the sediment-water interface. With this device, 

up-to-date information on benthic flux was added in the 

2004–06 study. Interpretation of the data generated by the new 

sampling device comes with some caveats. First, the device 

was designed to monitor changes in the chemical composition 

of water immediately above the lakebed sediments over 

time and to compare those results to concurrently sampled 

water 1 m above lakebed sediments. Second, the device did 

not measure gradients in the pore water or at the sedimentwater interface; the analytical results for the small volume 

sampled represent the net effect of all processes operating at 

the sediment-water interface. Third, no attempt was made to 

control oxidation of samples during sample processing; as 

such, the partitioning between dissolved and particulate phases 

cannot be assessed.

A summary of the analytical results obtained on 22 

sampling trips during the 2004–06 study are listed in table 12

for 8 constituents. All samples were obtained at pelagic station 

4, near the main channel in situ flux chamber study reported 

by Kuwabara and others (2000). Table 12 lists constituents 

with significantly higher median concentrations in sedimentwater interface samples than those in lower hypolimnetic 

samples (collected 1 m above the lakebed). Samples were 

compared using the paired Wilcoxon Signed-Ranks Test. 

No significant difference was apparent for paired median 

concentrations of dissolved inorganic nitrogen. Paired median 

concentrations of total phosphorus, dissolved organic carbon, 

total cadmium, total zinc, total iron, total lead, and total 

manganese were significantly higher in the sediment-water 

interface than in the lower hypolimnion. Of these seven 

analytes, the differences between the sediment-water interface 

and lower hypolimnion were, from smallest to largest: 

dissolved organic carbon, 1.2 times; total zinc, 1.8 times; total 

cadmium, 2.7 times; total phosphorus, 3.5 times; total iron, 12 

times; total lead, 19 times; and total manganese, 27 times.
32 Coeur d’Alene Lake, Idaho: Insights Gained From Limnological Studies of 1991–92 and 2004–06

Implications of Limnological Studies 

A number of implications can be gleaned from the 

results of the numerous water-quality monitoring studies 

in Coeur d’Alene Lake. Coeur d’Alene River is a source of 

dissolved and particulate phase metals to the lake, and existing 

lakebed sediments serve as a sink for particulate phase metals 

and a source of dissolved metals in the lake. Even though 

efforts are continuing in the Coeur d’Alene River basin to 

control metals contamination as part of the ROD, conditions in 

the lake with regard to metals cannot be expected to improve 

significantly if the river source and bed sediment source 

are not both addressed. In addition, wind-driven circulation 

patterns and riverine inflow plumes contribute to the spread 

of contaminants throughout the lake. Therefore, no part of the 

lake is immune to contamination.

Although the trophic state of the lake has been classified 

as oligotrophic or mesotrophic (depending on the variable 

used for classification) in both the 1991–92 and 2004–06 

studies, phosphorus concentrations and lake productivity have 

increased over time, and nitrogen-to-phosphorus ratios (when 

detected) appear to have decreased over time. Increased loads 

of nutrients to the lake (primarily nitrogen and phosphorus) 

can increase the growth of algae and aquatic plants. When this 

organic material decomposes, oxygen dissolved in the water 

is consumed. Depletion of dissolved oxygen concentrations 

in the bottom waters of the lake could lead to geochemical 

processes that increase the rate of release of mining associated 

metals contaminants (such as dissolved arsenic, cadmium, 

mercury, lead, and zinc) from lakebed sediments, as well as 

stored nutrients that would stimulate additional plant and algae 

growth in a self-perpetuating cycle that may be difficult or 

impossible to interrupt. These processes could increase risks 

to human health and adversely affect the environment and the 

economic and social welfare of the community.

Phosphorus limitation is currently keeping biomass low, 

and results of the ELCOM-CAEDYM simulation model show 

that diatoms, the current dominant phytoplankton in the lake, 

are kept in control by toxic levels of zinc (Hipsey and others, 

2006; Kuwabara and others, 2006). Zinc loads to the lake 

would have to decrease more than 1–2 orders of magnitude 

before any appreciable reduction in zinc toxicity would be 

noted. However, if nutrient loads continue to increase as zinc 

loads decrease, phytoplankton dominance in the lake may 

shift from diatoms (Bacillariophyceae) to a more diverse 

assemblage of green algae (Chlorophyceae) and nuisance or 

bloom-forming species of blue-greens (Cyanobacteria) which 

are more zinc-intolerant (Hipsey and others, 2006). Nutrient 

load management should be addressed as a component of a 

Lake Management Plan. 

Constituent and units Sample 

type Median

Range

n

Maximum Minimum

No significant difference between SWI and LH

Dissolved inorganic nitrogen LH 86 200 36 22

SWI 92 220 28 22

SWI significantly greater than LH

Total phosphorus LH 7.5 41 3.0 22

SWI 26 49 6.0 22

Dissolved organic carbon, mg/L LH 1.3 1.5 1.2 12

SWI 1.6 3.3 1.2 12

Total cadmium LH .32 .48 .22 22

SWI .85 1.6 .31 22

Total zinc LH 76 110 66 22

SWI 140 340 77 22

Total iron LH 54 310 19 22

SWI 630 1,600 58 22

Total lead LH 1.8 17 .54 22

SWI 35 120 2.5 22

Total manganese LH 5.9 40 2.5 22

SWI 160 830 6.6 22

Table 12. Medians and ranges of concentrations of selected constituents measured in lower 

hypolimnion and near sediment-water interface at pelagic station 4, Coeur d’Alene Lake, Idaho, 

water years 2004-06.

[Values are in micrograms per liter unless otherwise indicated. Sample type: SWI, sediment-water interface; LH, 

lower hypolimnion. Abbreviations: mg/L, milligram per liter; n, number of samples]
Summary 33

Future Monitoring and Research Needs

Water-quality conditions in the lake have a significant 

effect on lake biota, tourism, recreation, and quality of life 

for basin residents, including the Coeur d’Alene Indian 

Tribe. A number of phenomena recorded during the course of 

USGS and Tribe limnological studies discussed in this report 

merit further investigation to provide a more comprehensive 

understanding of the myriad of processes that affect waterquality conditions in Coeur d’Alene Lake.

The ELCOM-CAEDYM model could serve as a valuable 

tool for Coeur d’Alene Lake managers for simulating the 

response of the lake to various remediation strategies in the 

basin. A long-term, comprehensive monitoring plan would 

allow lake managers to monitor for future changes in waterquality conditions; to track the frequency, duration and extent 

of anoxia in the lake’s hypolimnion; to fill data gaps that 

could improve ELCOM-CAEDYM; and to measure the lake’s 

response to future remediation measures. Generally, previous 

monitoring programs have been designed to answer specific 

questions and have differed in scope, constituents sampled, 

analytical methods, and timing of sampling. If possible, any 

future monitoring program would benefit from consistency 

in terms of space, time, constituents sampled, and analytical 

methods used.

A possible monitoring program could include monthly 

sampling of four stations within the pelagic zone (stations 1, 4, 

5, and 6, or a new station between stations 3 and 4 in place of 

4), with samples collected from within the euphotic zone and 

hypolimnion. In addition, the program could include monthly 

or more frequent sampling at major inflows and the lake’s 

primary outflow (USGS gaging station 12415140, St. Joe 

River nr Chatcolet, Idaho; USGS gaging station 12413860, 

Coeur d’Alene River nr Harrison, Idaho; USGS gaging station 

12417598, Spokane River at Lake Outlet at Coeur d’Alene, 

Idaho) to track changes in loads and in the lake’s mass balance 

of selected constituents. Sampled constituents in the lake, 

at major inflows, and at the primary outflow could include 

algal biomass (cell counts), chlorophyll-a, total nitrogen, total 

phosphorus, total organic plus ammonia nitrogen, nitrite plus 

nitrate, dissolved ammonia, dissolved orthophosphate, major 

ions, trace metals including zinc, lead, and iron, total and 

dissolved organic carbon, suspended-sediment concentration, 

dissolved oxygen, water temperature, pH, conductivity, and 

turbidity. Continuous data collection through installation 

of a long-term system for real-time measurements of wind 

speed and direction, chlorophyll-a, and depth profiles of 

temperature, pH, conductivity, turbidity, dissolved oxygen, 

and zinc concentration in the lake would substantially enhance 

understanding of lake conditions and would allow better 

tracking and modeling of inflow plumes.

Data from both the 1991–92 and the 2004–06 USGS 

limnological studies have shown that littoral areas are 

statistically similar in water quality to pelagic areas and 

therefore do not need more extensive characterization. The 

inclusion of one or two representative littoral stations in a 

future monitoring program likely would be sufficient to track 

long-term changes in this area, unless land-use practices are 

suspected to cause near-shore alterations in water quality.

Some areas of the lake are prone to remobilization 

of dissolved metals from the bed sediments into the water 

column due to low dissolved oxygen concentrations during 

certain times of the year. This phenomenon could be tracked 

over time throughout the lake. In addition, the occurrence of 

nutrient sequestration by metals could be further investigated. 

For example, some phosphorus is bound to iron, resulting 

in decreased dissolved orthophosphate concentrations. A 

decrease in iron in the lake could result in increased dissolved 

orthophosphate. Sedimentation and burial rates of metals 

could be quantified to better understand the flux of particulate 

associated metals to sediments in various areas of the lake and 

to improve overall knowledge of metal transport, fate, and 

mass balance.

Although the St. Joe and Coeur d’Alene Rivers are major 

sources for nutrient loading to the lake, additional nutrient 

inputs from increased development along the shoreline and 

from ungaged tributaries have not been fully assessed over 

time. To effectively monitor and manage future nutrient 

inputs, this influence could be quantified using the ELCOMCAEDYM model and empirical variables and verified through 

point samples collected near suspected source locations and 

inflows.

Summary

Insights into the limnological functioning of 

Coeur d’Alene Lake were based on information developed 

from two large-scale limnological studies of the lake 

conducted during calendar years 1991–92 and water years 

2004–06. The fate and transport of water and associated 

constituents following their delivery into a lake are determined 

by the interactions of a myriad of physical, chemical, and 

biological processes operating in the lake over a wide range of 

spatial and temporal scales.

Differences in hydrologic conditions were largely 

responsible for interannual differences in loads delivered into 

and discharged from Coeur d’Alene Lake because streamflow 

is a key factor in the calculation of constituent load. Overall, 

the lake is a sink for total nitrogen, total phosphorus, total 

cadmium, total lead, and total zinc loads. Total nitrogen 

inflow and outflow loads decreased in-between the 1991–92 

and 2004–06 studies, primarily due to improvements in 

wastewater treatment processes and resulting decreases in total 

nitrogen concentrations in treatment plant effluent in major 

inflows to the lake. Total phosphorus inflow and outflow loads 

fluctuated with streamflow in both study periods, but loads 

relative to streamflow were higher in the 2004–06 study than 

the 1991–92 study because total phosphorus concentrations 

in gaged inflows were statistically higher in the latter study. 
34 Coeur d’Alene Lake, Idaho: Insights Gained From Limnological Studies of 1991–92 and 2004–06

Inflow trace-metal loads generally decreased between the 

1991–92 and 2004–06 studies, but differences in sampling 

design and analytical reporting limits between the studies 

prevented a robust and accurate comparison of loads.

Comparison of water temperatures and water column 

transparency among the 4 years and five pelagic stations 

indicated no significant changes in water column heating 

and convective circulation. However, thermocline depths 

throughout the lake were highly variable during the years 

studied.

No significant changes in dissolved oxygen 

concentrations between study periods were noted at any 

stations. Concentrations were significantly lower in the 

hypolimnion than in the euphotic zone at all stations. The 

highest concentrations at each station were measured in winter 

in association with minimum water temperatures. Minimum 

concentrations were measured in the hypolimnion of each 

station during late summer or autumn as prolonged thermal 

stratification restricted mixing of the oxygenated upper water 

column with the hypolimnion.

Increased chlorophyll-a and total phosphorus 

concentrations were measured throughout the lake in the 

2004–06 study compared with the 1991–92 study. No 

significant change was detected in hypolimnetic dissolved 

inorganic nitrogen concentrations between study periods. Total 

zinc, total cadmium, and total lead concentrations decreased 

from the 1991–92 study to the 2004–06 study everywhere 

except at pelagic station 6, where frequency of detection was 

low.

Large differences in median concentrations of dissolved 

inorganic nitrogen were measured in the euphotic zone and 

hypolimnion of the three deep stations (1, 3, and 4). These 

differences were attributable to several limnological processes, 

including seasonal inflow plume routing, isolation from winddriven circulation and associated hypolimnetic enrichment, 

phytoplanktonic assimilation during summer months, and 

benthic flux.

Median detected nitrogen-to-phosphorus ratios decreased 

from the 1991–92 study to the 2004–06 study. Whereas the 

lake was clearly phosphorus-limited in 1991–92, in 2004–06 

the lake may have been much closer to the boundary value 

of 7.2 that separates nitrogen from phosphorus limitation. 

However, due to changes in analytical reporting limits over the 

two studies, the data are insufficiently certain to draw reliable 

conclusions with regard to limiting nutrients.

For both studies, the trophic state of the lake was 

classified as oligotrophic, or less productive, with regard to 

total phosphorus and chlorophyll-a concentrations and as 

mesotrophic, or moderately productive, with regard to Secchidisc transparency depth.

The significant concentration gradients measured across 

the lake were:

• Dissolved inorganic nitrogen–gradient north and south 

radiating from central station 4 (high);

• Total phosphorus–gradient from south end (high) to 

north end (low);

• Total lead–gradient north and south radiating from 

central station 4 (high);

• Total zinc–gradient north and south radiating from 

central station 4 (high);

• Dissolved oxygen–gradient from north end (high) to 

south end (low); and

• Water column transparency–gradient from north end 

(high) to south end (low).

The southern end of the lake is a highly sensitive 

area that is subject to periodic anoxia, higher phosphorus 

concentrations, and higher turbidity. Although metals 

contamination is relatively low, the southern end of the lake 

is not completely isolated from metal-laden inflows from 

the Coeur d’Alene River or from wind-driven circulation 

of contaminated bed sediments from other parts of the lake. 

Higher lake productivity and hypolimnetic anoxia in this area 

will tend to remobilize any metals present in bed sediments.

Internal circulation from wind-generated waves and 

from changes in the thermocline is an important process for 

distribution of water-quality constituents throughout Coeur 

d’Alene Lake. Surficial distribution of trace metals throughout 

most of the lake, including the bays, is relatively uniform. 

Even south of the Coeur d’Alene River mouth, lakebed 

sediments are contaminated with trace metals. Generally, no 

significant difference was detected in water quality between 

the pelagic euphotic zone and littoral zone (when comparing 

pelagic stations to closest littoral stations), indicating a 

relatively uniform surficial distribution of constituents across 

the lake.

The fate and transport of constituents such as nutrients, 

trace metals, and sediment in and occasionally through Coeur 

d’Alene Lake are highly dependent on inflow-plume routing 

of the two primary inflow sources, the Coeur d’Alene and St. 

Joe Rivers. Most riverine inflows move through the lake as 

overflow during summer, interflow during spring and autumn, 

and underflow during winter. However, shallow depths in 

the southern part of the lake may have allowed full-depth, 

convective circulation and muted the median-concentration 

difference between the euphotic zone and lower hypolimnion 

for most analytes.
References Cited 35

Benthic flux experiments showed that movements of 

dissolved metals, nutrients, and dissolved organic carbon 

out of lakebed sediments in the deep part of the lake, likely 

are due to molecular diffusion. This outward benthic flux 

of dissolved materials is in contrast to the sedimentation of 

the same materials to lake sediments when associated with 

particulate material, meaning that the sediments may be a 

source for dissolved metals and nutrients while still being 

a sink for the same constituents in particulate form. When 

anoxic conditions are not already present at the sedimentwater interface, the transition from oxic to anoxic conditions 

occurred in the top 1–5 cm of bed sediments. In the transition 

zone, the reduction of manganese and ferric oxyhydroxides 

can result in the release of trace metals in the dissolved 

phase. When anoxic conditions are present at the sedimentwater interface (such as in the southern area of the lake), no 

transition zone is present, and trace metals may be released 

right at the interface and would be available for transport by 

physical limnological processes.

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38 Coeur d’Alene Lake, Idaho: Insights Gained From Limnological Studies of 1991–92 and 2004–06

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Appendixes 39

Appendix A. Analytical Data for Samples Collected at Pelagic and Littoral 

Stations in Coeur d’Alene Lake, Calendar Years 1991–92 

Data are available for download at http://pubs.usgs.gov/sir//2008/5168/AppendixA.xls

Appendix B. Analytical Data for Samples Collected at Pelagic and Littoral 

Stations in Coeur d’Alene Lake, Water Years 2004–06 

Data are available for download at http://pubs.usgs.gov/sir//2008/5168/AppendixB.xls

Appendix C. Selected Analytical Data for Quality-Control Samples Collected in 

Coeur d’Alene Lake, Water Years 2004–06 

Data are available for download at http://pubs.usgs.gov/sir//2008/5168/AppendixC.xls
40 Coeur d’Alene Lake, Idaho: Insights Gained From Limnological Studies of 1991–92 and 2004–06

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Manuscript approved for publication, September 15, 2008

Prepared by the USGS Publishing Network

Bill Gibbs 

Debra Grillo

Bobbie Jo Richey

Sharon Wahlstrom

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
Wood and Beckwith—Coeur d’Alene Lake, Idaho: Insights Gained from Limnological Studies of 1991–92 and 2004–06—Scientific Investigations Report 2008-5168