science for a changing world

Role of Limnological Processes in Fate and 

Transport of Nitrogen and Phosphorus Loads 

Delivered Into Coeur d'Alene Lake and Lake 

Pend Oreille, Idaho, and Flathead Lake, Montana

Professional Paper 1682

National Water-Quality Assessment Program

U.S. Department of the Interior 

U.S. Geological Survey
Cover photo: Rainy day at Lake Pend Oreille, Idaho, 1989. Turbid snowmelt plume from Clark Fork overflowing clear, dark lake 

water in vicinity of Warren Island/Hope Point just downstream from Clark Fork delta. View is to the northwest. Photo reproduced 

with permission from Michael A. Beckwith, May 1989.
Role of Limnological Processes in Fate and 

Transport of Nitrogen and Phosphorus 

Loads Delivered Into Coeur d'Alene Lake 

and Lake Pend Oreille, Idaho, and Flathead 

Lake, Montana

By Paul F. Woods

U.S. GEOLOGICAL SURVEY PROFESSIONAL PAPER 1682

NATIONAL WATER-QUALITY ASSESSMENT PROGRAM

2004
U.S. DEPARTMENT OF THE INTERIOR 

GALE A. NORTON, Secretary

U.S. GEOLOGICAL SURVEY 

Charles G. Groat, Director

Any use of firm, trade, and brand names in this report is for

identification purposes only and does not constitute

endorsement by the U.S. Government.

Library of Congress Cataloging in Publication Data

Woods, P.P.

Role of limnological processes in fate and transport of nitrogen and phosphorus loads 

delivered into Coeur d'Alene Lake and Lake Pend Oreille, Idaho, and Flathead Lake, 

Montana / by Paul F. Woods

p. cm. - (U.S. Geological Survey professional paper; 1682)

Includes bibliographical references (p.).

ISBN 0-607-95562-7 (alk. paper)

1. Limnology-ldaho-Coeur d'Alene Lake. 2. Nitrogen-Environmental 

aspects-ldaho-Coeur d'Alene Lake. 3. Phosphorus-Environmental aspects-ldaho-Coeur 

d'Alene Lake. 4. Limnology-ldaho-Pend Oreille, Lake. 5. Nitrogen-Environmental 

aspects-ldaho-Pend Oreille, Lake. 6. Phosphorus-Environmental aspects-ldaho-Pend 

Oreille, Lake. 7. Limnology-Montana-Flathead Lake. 8. Nitrogen-Environmental 

aspects-Montana-Flathead Lake. 9. Phosphorus-Environmental 

aspects-Montana-Flathead Lake. I. Title. II, Series

QJH1Q5J2W662QQ4______________________________

551.48'2-dc22 2003071042

For sale by U.S. Geological Survey Information Services

Box 25286, Federal Center

Denver, CO 80225-0286
FOREWORD

The U.S. Geological Survey (USGS) is committed to serve the Nation with accurate and timely scientific information that helps enhance and protect the overall quality of life, and facilitates effective management of water, biological, energy, and mineral resources (http://www.usgs.gov/). Information on the quality 

of the Nation's water resources is of critical interest to the USGS because it is so integrally linked to the 

long-term availability of water that is clean and safe for drinking and recreation and that is suitable for 

industry, irrigation, and habitat for fish and wildlife. Escalating population growth and increasing demands 

for the multiple water uses make water availability, now measured in terms of quantity and quality, even 

more critical to the long-term sustainability of our communities and ecosystems.

The USGS implemented the National Water-Quality Assessment (NAWQA) Program to support 

national, regional, and local information needs and decisions related to water-quality management and policy (http://water.usgs.gov/nawqa/). Shaped by and coordinated with ongoing efforts of other Federal, State, 

and local agencies, the NAWQA Program is designed to answer: What is the condition of our Nation's 

streams and ground water? How are the conditions changing over time? How do natural features and 

human activities affect the quality of streams and ground water, and where are those effects most pronounced? By combining information on water chemistry, physical characteristics, stream habitat, and 

aquatic life, the NAWQA Program aims to provide science-based insights for current and emerging water 

issues and priorities. NAWQA results can contribute to informed decisions that result in practical and 

effective water-resource management and strategies that protect and restore water quality.

Since 1991, the NAWQA Program has implemented interdisciplinary assessments in more 

than 50 of the Nation's most important river basins and aquifers, referred to as Study Units 

(http://water.usgs.gov/nawqa/nawqamap.html). Collectively, these Study Units account for more than 

60 percent of the overall water use and population served by public water supply, and are representative of the Nation's major hydrologic landscapes, priority ecological resources, and agricultural, 

urban, and natural sources of contamination.

Each assessment is guided by a nationally consistent study design and methods of sampling and 

analysis. The assessments thereby build local knowledge about water-quality issues and trends in a 

particular stream or aquifer while providing an understanding of how and why water quality varies 

regionally and nationally. The consistent, multi-scale approach helps to determine if certain types of 

water-quality issues are isolated or pervasive, and allows direct comparisons of how human activities and 

natural processes affect water quality and ecological health in the Nation's diverse geographic and environmental settings. Comprehensive assessments on pesticides, nutrients, volatile organic compounds, trace 

metals, and aquatic ecology are developed at the national scale through comparative analysis of the StudyUnit findings (http://water.usgs.gov/nawqa/natsyn.html).

The USGS places high value on the communication and dissemination of credible, timely, and relevant science so that the most recent and available knowledge about water resources can be applied in management and policy decisions. We hope this NAWQA publication will provide you the needed insights and 

information to meet your needs, and thereby foster increased awareness and involvement in the protection 

and restoration of our Nation's waters.

The NAWQA Program recognizes that a national assessment by a single program cannot address all 

water-resource issues of interest. External coordination at all levels is critical for a fully integrated understanding of watersheds and for cost-effective management, regulation, and conservation of our Nation's 

water resources. The Program, therefore, depends extensively on the advice, cooperation, and information 

from other Federal, State, interstate, Tribal, and local agencies, non-government organizations, industry, 

academia, and other stakeholder groups. The assistance and suggestions of all are greatly appreciated.

Robert M. Hirsch 

Associate Director for Water

Foreword iii
iv Fate and Transport of Nitrogen and Phosphorus, Coeur d'Alene Lake, Lake Pend Oreille, and Flathead Lake
CONTENTS

Foreword................................................................................ iii

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

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

Overview of National Water-Quality Assessment Program...................................... 2

Overview of Northern Rockies Intermontane Basins study area .................................. 3

Purpose and scope. ..................................................................... 6

Description of drainage basins ............................................................... 6

Coeur d'Alene Lake .................................................................... 6

Flathead Lake ......................................................................... 7

Lake Pend Oreille...................................................................... 8

Evaluation approach ....................................................................... 9

Nutrient loads ............................................................................ 9

Overview............................................................................. 9

Coeur d'Alene Lake .................................................................... 10

Flathead Lake ......................................................................... 11

Lake Pend Oreille...................................................................... 12

Among-lake comparisons................................................................ 13

Physical limnology ........................................................................ 14

Overview. ............................................................................ 14

Among-lake comparisons................................................................ 16

Coeur d'Alene Lake .................................................................... 17

Flathead Lake ......................................................................... 23

Lake Pend Oreille...................................................................... 23

Chemical and biological limnology ........................................................... 25

Overview............................................................................. 25

Trophic state.......................................................................... 26

Hypolimnetic nutrient storage ............................................................ 27

Nutrient partitioning.................................................................... 28

Epilimnion and hypolimnion .......................................................... 28

Inflow loads and outflow loads ........................................................ 30

Fate and transport of nutrient loads............................................................ 37

Overview .......................................................................... 37

Coeur d'Alene Lake.................................................................. 38

Flathead Lake....................................................................... 39

Lake Pend Oreille ................................................................... 40

Summary and conclusions. .................................................................. 41

References cited .......................................................................... 42

FIGURES

1-4. Maps showing:

1. Location of the Northern Rockies Intermontane Basins study area, selected dams, selected 

U.S. Geological Survey gaging stations, Indian Reservations, and Glacier National Park, 

Montana, Idaho, and Washington .................................................. 4

2. Bathymetry and locations of selected limnological stations, Coeur d'Alene Lake, Idaho ....... 18

3. Bathymetry and locations of selected limnological stations, Flathead Lake, Montana.......... 19

4. Bathymetry and locations of selected limnological stations, Lake Pend Oreille, Idaho ......... 20

Contents v
5-6. Graphs showing:

5. Annual mean percentage composition of bioavailable and participate nitrogen and phosphorus concentrations, in relation to total nitrogen and phosphorus concentrations, respectively, 

within the epilimnion and hypolimnion at the deepest limnological stations, Coeur d'Alene 

Lake and Lake Pend Oreille, Idaho, and Flathead Lake, Montana ......................... 29

6. Annual mean percentage composition of bioavailable and particulate nitrogen and phosphorus concentrations, in relation to total nitrogen and phosphorus concentrations, 

respectively, for inflows and outflows, Coeur d'Alene Lake and Lake Pend Oreille, Idaho, 

and Flathead Lake, Montana ...................................................... 31

7-11. Diagrams showing:

7. Relation between inputs and outputs of total nitrogen and phosphorus and nutrient

partitioning of input and output loads, Coeur d'Alene Lake, Idaho, 1991 calendar year ........ 32

8. Relation between inputs and outputs of total nitrogen and phosphorus and nutrient

partitioning of input and output loads, Coeur d'Alene Lake, Idaho, 1992 calendar year ........ 33

9. Relation between inputs and outputs of total nitrogen and phosphorus and nutrient

partitioning of input and output loads, Flathead Lake, Montana, 1978-82. .................. 34

10. Relation between inputs and outputs of total nitrogen and phosphorus and nutrient

partitioning of input and output loads, Lake Pend Oreille, Idaho, 1989 water year ............ 35

11. Relation between inputs and outputs of total nitrogen and phosphorus and nutrient

partitioning of input and output loads, Lake Pend Oreille, Idaho, 1990 water year ............ 36

TABLES

1. Annual input, output, and retained loads of total nitrogen and phosphorus, Coeur d'Alene

Lake, Idaho, calendar years 1991 and 1992 .............................................. 11

2. Mean annual input, output, and retained loads of total nitrogen and phosphorus, Flathead

Lake, Montana, 1978-82 ............................................................ 12

3. Annual input, output, and retained loads of total nitrogen and phosphorus, Lake Pend Oreille,

Idaho, water years 1989 and 1990 ..................................................... 13

4. Average of retained load/input load for total nitrogen and phosphorus, Coeur d'Alene Lake and

Lake Pend Oreille, Idaho, and Flathead Lake, Montana. .................................... 14

5. Physical limnological characteristics, Coeur d'Alene Lake and Lake Pend Oreille, Idaho, and

Flathead Lake, Montana ............................................................. 16

6. Trophic-state classification based on open-boundary values for four limnological variables ........ 26

7. Trophic state of Coeur d'Alene Lake and Lake Pend Oreille, Idaho, and Flathead Lake, Montana,

based on annual mean values for four limnological variables ................................ 27

8. Annual mean concentrations of total nitrogen and phosphorus within the epilimnion and hypolimnion at the deepest limnological stations, Coeur d'Alene Lake and Lake Pend Oreille, Idaho, 

and Flathead Lake, Montana. ......................................................... 28

9. Summary of retained load/input load for total nitrogen and phosphorus and selected physical

limnological characteristics, Coeur d'Alene Lake and Lake Pend Oreille, Idaho, and Flathead Lake, 

Montana ......................................................................... 37

vi Fate and Transport of Nitrogen and Phosphorus, Coeur d'Alene Lake, Lake Pend Oreille, and Flathead Lake
CONVERSION FACTORS, VERTICAL DATUM, AND ABBREVIATED WATER-QUALITY UNITS

Multiply

centimeter (cm) 

cubic kilometer (km-5 ) 

cubic meter per second (m-Vs)

kilogram (kg)

kilometer (km)

meter (m)

meter per year (m/yr) 

square kilometer (km2)

By

0.3937 

0.2399 

35.31

2.205

0.6214

3.281

3.281 

0.3861

To obtain

inch (in.) 

cubic mile (mi-5 ) 

cubic foot per second (ft-Vs)

pound (Ib)

mile (mi)

foot (ft)

foot per year (ft/yr) 

square mile (mi2)

To convert °C (degrees Celsius) to °F (degrees Farenheit), use the following equation:

°F = (1.8°C) + (32)

Sea level: In this report, "sea level" refers to the National Geodetic Vertical Datum of 1929 (NGVD of 1929)—a 

geodetic datum derived from a general adjustment of the first-order level nets of the United States and Canada, formerly called Sea Level Datum of 1929.

Abbreviated water-quality units

|ag/L microgram per liter

|am micrometer

mg/L milligram per liter

mg/kg milligram per kilogram

Contents vii
viii Fate and Transport of Nitrogen and Phosphorus, Coeur d'Alene Lake, Lake Pend Oreille, and Flathead Lake
Role of Limnological Processes in Fate and 

Transport of Nitrogen and Phosphorus Loads 

Delivered Into Coeur d'Alene Lake and Lake Pend 

Oreille, Idaho, and Flathead Lake, Montana

By Paul F. Woods

Abstract

The fate and transport of nutrient loads, following their delivery into a lake, result from the 

integration of all hydrologic, physical, chemical, 

and biological processes that operate within that 

lake. If only empirical relations such as areal water 

load, hydraulic residence time, trap efficiency, and 

mean depth are used to estimate nutrient fate and 

transport without consideration of the other complex limnological processes involved, the magnitude of nutrient retention by the lake may be incorrectly predicted. The nutrient retentions empirically predicted for northern Idaho's Coeur d'Alene 

Lake and Lake Pend Oreille and northwestern 

Montana's Flathead Lake did not agree with the 

nutrient retentions measured for the three lakes on 

the basis of quantitative differences between input 

and output loads.

The three lakes are within the 81,600-squarekilometer Northern Rockies Intermontane Basins 

study area, which was added in 1996 to the U.S. 

Geological Survey's National Water-Quality 

Assessment Program. The lakes were selected for 

evaluation of nutrient fate and transport because 

they are affected by nutrient enrichment, their 

input and output nutrient loads had been quantified, and their limnological characteristics had 

been extensively studied.

The three lakes represent a broad range in 

physical limnological characteristics, which can be 

expected to influence the fate and transport of 

nutrients within the lakes. Lake volumes range 

from 2.8 (Coeur d'Alene Lake) to 53.9 (Lake Pend 

Oreille) cubic kilometers. Lake Pend Oreille is the

deepest (357 meters), and Coeur d'Alene Lake is 

the shallowest (63.7 meters). Coeur d'Alene Lake 

has the shortest hydraulic residence time (lake volume divided by mean annual outflow volume), 

0.50 year; the other two lakes have longer hydraulic residence times—2.2 years for Flathead Lake 

and 2.4 years for Lake Pend Oreille.

The annual loads of nutrients delivered into 

the three lakes from drainage basin and atmospheric sources varied widely; total nitrogen loads 

ranged from 945,000 to 5,670,000 kilograms, and 

total phosphorus loads ranged from 43,600 to 

408,000 kilograms. Lake Pend Oreille received 

and discharged the largest loads of both nutrients; 

Coeur d'Alene Lake received and discharged the 

smallest loads. Coeur d'Alene Lake and Lake 

Pend Oreille retained about 15 percent of the total 

nitrogen loads they received; Flathead Lake retained about one-third of the nitrogen load it received. The retention of total phosphorus was 

much different for Coeur d'Alene and Flathead 

Lakes; respectively, they retained about one-half 

and three-fourths of the phosphorus loads they 

received. Lake Pend Oreille retained less than 

about 17 percent of the total phosphorus load it 

received.

If only morphometric values such as mean 

depth and maximum depth were considered, the 

lake with the largest values, Lake Pend Oreille, 

would be expected to retain the largest percentage 

of total nitrogen and phosphorus loads received. 

The unexpected small retention of both nutrients, 

particularly phosphorus, by Lake Pend Oreille 

indicated that limnological processes other than 

just physical sedimentation were affecting the fate

Abstract 1
and transport of nutrient loads delivered to that 

lake.

Nutrient retention, or the lack thereof, was 

strongly related to circulation processes, in a spatial and temporal context, in the three lakes. The 

inflow plumes from their primary tributaries were 

routed primarily as overflow, especially during 

snowmelt runoff, when each lake received most of 

its annual loads of total nitrogen and phosphorus. 

The long, narrow shape of Coeur d'Alene Lake, 

along with its short hydraulic residence time, was 

not empirically predictive of nutrient retention. In 

contrast, the other two lakes were much deeper, 

had much larger and wider basins, and had hydraulic residence times longer than 2 years; all of 

which would predict substantial retention of nutrients. Inflow-plume routing in Flathead Lake during snowmelt runoff tended to follow a lengthy 

and somewhat circular path, both favorable to 

retention. Inflow-plume routing of snowmelt runoff in Lake Pend Oreille was directed primarily 

into the shallow northern basin that leads to the 

lake's outlet, not into the deep southern basin with 

its large retentive capacity for nutrients. The formation of a thermal bar along the approximate 

boundary between the shallow and deep basins of 

Lake Pend Oreille was postulated as a major cause 

of its small retention of nutrients.

The influence of chemical and biological processes, in addition to physical processes, was evident in each of the lakes on the basis of differences 

in partitioning of nutrients between the bioavailable (dissolved) and particulate fractions in input 

and output loads. Input and output loads of total 

nitrogen in Coeur d'Alene Lake differed little in 

their proportions of bioavailable and particulate 

nitrogen. Of the total nitrogen input to Flathead 

Lake, 42 percent was bioavailable; that proportion 

had declined to 23 percent at the lake's outlet. The 

proportion of bioavailable nitrogen in Lake Pend 

Oreille was comparable to that in Flathead Lake, 

but the average proportion declined from 36 percent at the lake's inlet to 24 percent at the outlet. 

The shifts in partitioning of nitrogen were attributable in part to phytoplankton assimilation of bioavailable nitrogen in each of the lakes. In Coeur 

d'Alene Lake, the addition of bioavailable nitrogen from a substantial benthic flux was an important internal source.

Input and output proportions of bioavailable 

and particulate phosphorus differed little in Coeur 

d'Alene Lake, even though the lake retained about 

50 percent of its total phosphorus input load. Nutrient partitioning and retention in Flathead Lake 

were comparable to those in Coeur d'Alene Lake, 

except that Flathead Lake retained about 75 percent of its input load of phosphorus. The output 

proportion of bioavailable phosphorus in Lake 

Pend Oreille was slightly smaller than the input 

proportion. The lack of substantial shifts in partitioning of phosphorus between input and output 

loads, despite substantial sedimentation of input 

loads, was attributable both to the propensity of 

bioavailable phosphorus to sorb to inorganic and 

organic particulates and to the production of particulate phosphorus as a result of phytoplankton 

assimilation of bioavailable phosphorus.

The primary determinants of the fate and 

transport of nutrients in these three lakes were 

physical limnological processes such as inflowplume routing and sedimentation. However, the 

evaluation of chemical and biological processes 

was essential to decipher how the fate and transport of nutrients were altered within each lake.

INTRODUCTION

Overview of National Water-Quality Assessment Program

Industry and government have made substantial 

financial investments over the past several decades with 

the intent to improve water quality across the Nation; 

despite these efforts, numerous water-quality issues 

remain. To provide consistent and scientifically sound 

information for managing the Nation's water resources, 

the U.S. Geological Survey (USGS) began full-scale 

implementation of a National Water-Quality Assessment (NAWQA) Program in 1991. The long-term goals 

of the NAWQA Program are to (1) provide a nationally

2 Fate and Transport of Nitrogen and Phosphorus, Coeur d'Alene Lake, Lake Pend Oreille, and Flathead Lake
consistent description of current water-quality conditions for a large part of the Nation's water resources, 

(2) detect long-term trends (or lack of trends) in water 

quality, and (3) identify and describe major factors that 

affect observed water-quality conditions and trends 

(Hirsch and others, 1988). The design of the program 

enables integration of information into a nationally 

consistent data base for comparisons of water-quality 

data over a large range of geographic and hydrologic 

conditions. Fifty-two NAWQA study areas, comprising 

many of the Nation's most important river basins and 

aquifer systems, have been investigated since the program started in 1991.

Overview of Northern Rockies Intermontane 

Basins Study Area

The Northern Rockies Intermontane Basins 

(NROK) study area was selected by the USGS for 

inclusion in the NAWQA Program for the following 

four reasons: (1) the area includes several important 

river systems; (2) land use/land cover in the area is a 

mixture of forested, agricultural, urban, and developing 

areas; (3) the area contains major sole-source aquifers 

such as the Spokane Valley/Rathdrum Prairie and Missoula Valley aquifers; and (4) mining practices have 

affected the quality of streams and aquifers (Tornes, 

1997). Extensive consultation with water-resource 

managers, planners, State and local governments, and 

citizen groups identified five high-priority, regionalscale, water-quality issues within the NROK study 

area: (1) toxic trace elements in surface water and 

ground water; (2) nutrients in surface water and ground 

water from point and nonpoint sources; (3) degradation 

of surface water and ground water from urban areas 

and suburban development; (4) sedimentation from 

timber harvesting and agriculture; and (5) effects of 

these inputs on aquatic biological communities (Tornes, 

1997). The USGS began study activities in the NROK 

study area in late 1996.

The NROK study area is situated in western 

Montana, northern Idaho, and eastern Washington and 

encompasses 81,600 km2 (fig. 1). The Clark Fork-Pend 

Oreille River Basin constitutes about 79 percent of the 

area; the Spokane River Basin constitutes the remainder. The study area lies entirely within the Columbia 

River Basin and Northern Rocky Mountains physiographic provinces. Topography ranges from high, 

mountainous areas to large, flat-lying valleys. Elevations range from about 3,000 m in the mountains and 

about 1,700 m in the mountain valleys of western Montana to about 460 m along the Spokane River in eastern 

Washington. The intermontane basins of western Montana receive as little as 38 cm of precipitation annually, 

whereas the area near the Continental Divide in northwestern Montana receives more than 250 cm of precipitation (Maret and Dutton, 1999). Snowmelt from April 

to July generates most of the annual runoff in the study 

area (Kendy and Tresch, 1996).

The Clark Fork originates in southwestern 

Montana near Butte and flows northwestward about 

560 km to Lake Pend Oreille in northern Idaho. The 

Pend Oreille River exits the lake and flows northward 

to join the Columbia River in Canada. The mean 

annual streamflow of the Pend Oreille River near the 

United States-Canadian border is about 790 m3/s 

(Tornes, 1997). The Clark Fork's major tributaries, in 

downstream order, are the Blackfoot, Bitterroot, and 

Flathead Rivers. Within northern Idaho, the Coeur 

d'Alene and St. Joe Rivers are the two principal tributaries to Coeur d'Alene Lake, which is drained by the 

Spokane River. The Spokane River flows westward and 

enters the Columbia River in eastern Washington. The 

mean annual streamflow at the USGS gaging station 

Spokane River at Spokane, Washington (station 5, 

fig. 1), is about 200 m3/s (Tornes, 1997).

The NROK study area contains numerous large, 

natural lakes and reservoirs. The Clark Fork-Pend 

Oreille River Basin contains Hungry Horse Reservoir, 

Flathead Lake, Lake Pend Oreille, and Priest Lake; the 

Spokane River Basin contains Coeur d'Alene Lake 

(fig. 1). Flathead Lake is the largest natural freshwater 

lake in the Western United States; Lake Pend Oreille is 

the 21st-largest and fifth-deepest freshwater lake in the 

United States (Bue, 1963). These five water bodies significantly influence the hydrology and water quality of 

the NROK study area; their combined volume, about 

87 km3 , represents more than 3 times the combined 

annual discharge, about 28 km3 , delivered to the 

Columbia River by the Pend Oreille and Spokane 

Rivers.

Several of the high-priority, regional-scale, waterquality issues listed by Tornes (1997) for the NROK 

study area have affected Coeur d'Alene and Flathead 

Lakes and Lake Pend Oreille. Nutrients from point and 

nonpoint sources have led to concerns about nutrient 

enrichment and potential eutrophication of all three 

lakes. Historical mining, ore-processing, and tailingsdisposal activities in the study area have led to substanIntroduction 3
CANADA 

UNITED STATES

KALISPELL

INDIAN 

RESERVATION

Pinehurst

/ Bunker Hill 

Superfund Site

48"—— -^-C^VJhi-v-' 

)SPOKANE INDIAN-"

\£"\ RESER- J

"\

BRITISH 

r—-—COLUMBIA

- - River (

ALBERTA

? WASHINGTON

h 1 Columbia^-—— -\Stlldy

OREGON IDAHO

MONTANA

...J

Base from U.S. Geological Survey digital data. 

Hydrologic unit maps, 1:100,000,1994; rivers 

and streams, 1:250,000,1994; Albers EqualArea Projection. Standard parallels 46° 00', 

48° 30', and 115° 00', 45° 00'. No false easting 

or false northing

Figure 1. Location of the Northern Rockies Intermontane Basins study area, selected dams, selected U.S. Geological Survey 

gaging stations, Indian Reservations, and Glacier National Park, Montana, Idaho, and Washington.

4 Fate and Transport of Nitrogen and Phosphorus, Coeur d'Alene Lake, Lake Pend Oreille, and Flathead Lake
CANADA 

UNITED STATES

SITE 

NUMBER

EXPLANATION

I___I Superfund study area 

—.. —— Basin boundary

A U.S. Geological Survey 

4 gaging station and 

site number

Kerr Dam Dam and name

U.S. GEOLOGICAL SURVEY GAGING STATIONS

GAGING STATION IDENTIFICATION 

NUMBER AND NAME

12388700 Flathead River at Perma, Montana

12413500 Coeur d'Alene River near Cataldo, Idaho

12413860 Coeur d'Alene River near Harrison, Idaho

12419000 Spokane River near Post Falls, Idaho

12422500 Spokane River at Spokane, Washington

12392000 Clark Fork at Whitehorse Rapids, near

	Cabinet, Idaho 

12395500 Pend Oreille River at Newport, Washington

0 10 20 30 40 50 KILOMETERS

i i i i i i

10 20 30 MILES

Introduction 5
tial trace-element contamination of terrestrial, riparian, 

and riverine habitats (Idaho Department of Environmental Quality, 2001; URS Greiner Inc., and CH2MHill Inc., 2001a) upstream from Coeur d'Alene Lake 

and Lake Pend Oreille. The NROK study area contains 

two of the Nation's largest Superfund sites, the Clark 

Fork Superfund site in the Clark Fork-Pend Oreille 

River Basin and the Bunker Hill Superfund site in the 

Spokane River Basin (fig. 1).

Despite these water-quality issues and the importance of these lakes to the hydrology of the NROK 

study area, no limnological sampling was conducted 

by the NAWQA Program within the NROK study area. 

That lack of limnological sampling reflected the 

NAWQA Program's decision not to study water quality 

in lakes and reservoirs for any of the 52 study areas; 

that decision was based primarily on budgetary constraints. The planning phase of the NAWQA Program, 

begun in 1986, resulted in a national program that was 

an aggregation of individual study areas in key river 

basins and aquifer systems. The program design emphasized a multitude of physical, chemical, and biological measurements over multiyear and decadal timescales. The high cost of conducting limnological sampling according to the NAWQA Program design 

resulted in the decision to target only freshwater 

streams and aquifers.

The desirability for limnological evaluation of 

lakes in the NROK study area became evident for several reasons as the study team reviewed historical data 

and published reports for the study area. First, several 

of the lakes were likely to significantly affect downstream water quality because of their very large volume 

in relation to annual discharge. Second, several of the 

lakes have been studied extensively over the past two 

decades. Substantial riverine loading data for nutrients 

are available for Coeur d'Alene and Flathead Lakes 

and Lake Pend Oreille; evaluation of these data revealed a distinct lake effect on the relation between 

inflow and outflow loads. Besides riverine loading 

data, these three lakes also have been sampled extensively for physical, chemical, and biological characteristics that would be useful for evaluating limnological 

effects on constituent transport. Third, each of the three 

lakes receives more than 85 percent of its annual inflow 

of water from a single tributary (Flathead Lake and 

Lake Pend Oreille) or two tributaries (Coeur d'Alene 

Lake). In lieu of NAWQA-funded limnological sampling of lakes in its study area, the NROK study team 

devised this analysis as an alternative approach for

their evaluation of the effects of lakes on constituent 

transport.

Purpose and Scope

The purpose of this report is to describe the role 

of limnological processes in determining the fate and 

transport of nutrients delivered into and discharged 

from three large, natural lakes within the NROK study 

area. Coeur d'Alene and Flathead Lakes and Lake Pend 

Oreille represent a broad range in physical limnological characteristics, which can be expected to significantly influence the fate and transport of nutrients 

delivered into the lakes. The study approach was to 

evaluate the substantial amount of historical limnological and riverine loading data for these three lakes. The 

initial phase of the evaluation was quantification of inflow and outflow loads of nutrients; subsequent phases 

of the evaluation focused on the influence of physical, 

chemical, and biological processes on in-lake distribution and pardoning of nutrients. Information gained 

from this study of the cumulative limnological processes influencing nutrients in the NROK lakes will 

benefit future lake-assessment studies and activities 

designed to manage and protect lake and reservoir 

quality.

DESCRIPTION OF DRAINAGE BASINS

Coeur d'Alene Lake

Coeur d'Alene Lake, Idaho's second largest, 

is located in northern Idaho within the 17,300-km2 

Spokane River Basin. The lake occupies the drowned 

river valley of the Pleistocene Spokane River and its 

two principal tributaries, the Coeur d'Alene and St. Joe 

Rivers. The valley was dammed by infilling of the 

present Rathdrum Prairie-Spokane River Valley with 

about 100 m of coarse gravel deposits during a series 

of glacial outburst floods from Lake Missoula between 

about 18,000 and 13,000 years ago (URS Greiner Inc., 

and CH2M-Hill Inc., 200 Ib). Present-day Coeur 

d'Alene Lake is about 35 km long in a north-south 

orientation and has a maximum width of about 3.7 km 

and a maximum depth of about 64 m. The lake covers 

129 km2 and has a volume of 2.8 km3 at its full-pool

6 Fate and Transport of Nitrogen and Phosphorus, Coeur d'Alene Lake, Lake Pend Oreille, and Flathead Lake
elevation of 648.7 m. The southern end of the lake is 

contiguous with four shallow lakes that were flooded in 

1906 by impoundment of the Spokane River by Post 

Falls Dam at Post Falls. The dam provides hydroelectric power, flood control, and irrigation supply.

Coeur d'Alene Lake receives surface-water inflow 

from a 9,690-km2 drainage area. About 90 percent of 

that inflow is delivered by the Coeur d'Alene and St. 

Joe Rivers (Woods and Beckwith, 1997); the lake is 

drained by the Spokane River, a tributary to the Columbia River. The Coeur d'Alene and St. Joe Rivers arise 

within the Coeur d'Alene and St. Joe Mountains, 

respectively. Much of the lake's drainage area is characterized by high, massive mountains and deep, intermontane valleys. Elevations range from about 650 m 

above sea level at the lake outlet to about 2,090 m at the 

Idaho-Montana border. About 75 percent of the drainage's land cover is forest (coniferous, sparse, or recovering harvest); rangeland and agriculture account for 

about 7 and 5 percent, respectively (Woods and Beckwith, 1997).

The lake's drainage basin receives some of the 

largest amounts of precipitation in Idaho. Basin topography affects the areal distribution of precipitation. 

Mean annual precipitation is about 64 cm at the lake, 

whereas mean annual precipitation is about 97 cm at 

Wallace, about 75 km east and 250 m higher in elevation than the lake. About 70 percent of the annual precipitation is snow during October to April. The influence of Pacific Maritime conditions can produce large 

rain-on-snow events during the winter. Although winter 

temperatures at Coeur d'Alene Lake are often below 

freezing, the lake normally does not freeze except at 

the shallow southern end.

The Coeur d'Alene River (drainage area 

3,810 km2) discharges into the southern third of the 

lake. Land-use activities in the drainage basin include 

recreation, logging, agriculture, and mining and ore 

processing. Most of the mining and ore-processing 

activities are in the drainage basin of the South Fork 

Coeur d'Alene River, which contains the Bunker Hill 

Superfund site (fig. 1). The St. Joe River (drainage area 

4,520 km2) discharges into the extreme southern end of 

the lake. Recreation and logging are the dominant land 

uses; little mining activity has occurred in this basin. 

Urban land use in the two basins is less than 1 percent 

(Woods and Beckwith, 1997).

Considerable concern exists about the potential 

for nutrient enrichment and subsequent eutrophication 

of Coeur d'Alene Lake because of land-use activities

within its drainage basin and near its shoreline, in addition to intensive recreational use of the lake (Woods 

and Beckwith, 1997). A 1975 nutrient load study, done 

as part of the National Eutrophication Survey, led to the 

conclusion that Coeur d'Alene Lake was mesotrophic, 

or moderately productive (U.S. Environmental Protection Agency, 1977). A second concern is the large 

amount of trace elements that have been introduced 

into Coeur d'Alene Lake as a consequence of more 

than 100 years of mining and ore-processing activities 

in the Coeur d'Alene River Basin (Woods and Beckwith, 1997). About 85 percent of the bottom of Coeur 

d'Alene Lake is substantially enriched in antimony, 

arsenic, cadmium, copper, lead, mercury, silver, and 

zinc (Horowitz and others, 1993, 1995).

Flathead Lake

The Flathead Lake and River Basin, at the confluence with the Clark Fork, cover about 18,400 km2 

of northwestern Montana and southeastern British 

Columbia, Canada. Flathead Lake lies in a tectonic 

graben basin that underwent extensive glaciation during the Pleistocene; the lake was formed by moraines 

at the western and southern boundaries of the last ice 

advance and is probably a remnant of a larger glacial 

lake system (Moore and others, 1982). The present-day 

lake is about 56 km long and has a maximum width of 

about 26 km and a maximum depth of about 113m. 

The lake's 300-km shoreline is often steep and rocky, 

especially along the eastern shore. The lake covers 

496 km2 and has a volume of 23.2 km3 at its full-pool 

elevation of 879 m. The lake's surface elevation was 

raised about 3.4 m by completion of Kerr Dam in the 

1930's. The dam, about 7 km downstream from the 

lake's natural outlet, is operated for flood control and 

hydropower purposes.

The Flathead River is the lake's major tributary; it 

enters the lake at the shallow northern end. At its 

inflow to the lake, the Flathead River drains about onehalf of the Flathead Lake and River Basin. Inflow from 

other tributaries increases the drainage area of Flathead 

Lake to about 11,400 km2 at its outlet. The lake is 

drained at the shallow southern end by the Flathead 

River, which is the largest tributary to the Clark Fork.

Most of the basin's northern, northwestern, and 

eastern regions are characterized by high, rugged 

mountains interspersed with deep, intermontane valDescription of Drainage Basins 7
leys. The southern and southwestern regions are dominated by the Flathead Valley, which contains Flathead 

Lake. Elevations range from about 880 m at the lake 

outlet to more than 3,000 m in Glacier National Park 

along the basin's eastern boundary. The dominant land 

cover in the basin's high mountain region is coniferous 

forest, whereas the dominant land cover in the Flathead 

Valley and adjacent foothills is grasses and, in drier 

areas, sagebrush. Logging is the dominant land use in 

the mountainous areas of the basin. Within the Flathead 

Valley, agriculture is an important land use, along with 

urban and rural development. Recreation is also an 

important land use in the basin because about 60 percent of the basin's area is contained within Glacier 

National Park and National Forest wilderness and 

roadless areas.

Climatic conditions in the basin are dominated 

by Pacific Maritime influences; however, cold airmasses of continental origin occasionally affect the 

area in the winter. At the lake, mean annual precipitation is about 50 cm; along the Continental Divide, it is 

about 250 cm. Most of the annual precipitation is snow 

during the winter. Flathead Lake's substantial heatstorage capacity influences local weather conditions by 

moderating air temperatures and increasing precipitation to the east of the lake. Although winter air temperatures are often below freezing, the lake normally does 

not freeze over for any appreciable period, primarily 

because of its very large volume and wind-induced 

turbulence.

Eutrophication is the primary water-quality issue 

for Flathead Lake (Stanford and others, 1997). Nutrient 

loadings to the lake originate from a combination of 

drainage basin and nearshore sources. The extensive 

road network developed for logging has contributed 

sediment and associated nutrients to the lake. Farming 

and grazing in the Flathead Valley are also sources of 

sediment and nutrients to the lake. Residential development around the lake's shoreline and its adjacent drainages has increased nutrient loadings from nonpoint 

sources, as well as from municipal wastewater-treatment facilities.

Lake Pend Oreille

Lake Pend Oreille is Idaho's largest lake. The lake 

is located in northern Idaho and is an important feature 

of the 64,300-km2 Clark Fork-Pend Oreille River Basin.

The lake lies in a glacially scoured graben, the southern 

end of which was plugged by massive deposition of 

sediments transported by catastrophic glacial outburst 

floods from Lake Missoula during the late Pleistocene 

(Molenaar, 1988). The deep, U-shaped basin of the lake 

separates three mountain ranges: the Cabinet, the Selkirk, and the Coeur d'Alene. Albeni Falls Dam, on the 

Pend Oreille River (fig. 1), was completed in 1952 and 

increased the lake's normal surface elevation by 4.3 m. 

The dam is operated to provide hydroelectric power, 

flood control, navigation, recreation, and fish and wildlife conservation. Present-day Lake Pend Oreille, 

including its outlet arm behind Albeni Falls Dam, is 

about 110 km long and has a maximum width of about 

10.8 km and a maximum depth of about 357 m. The 

lake and its outlet arm cover 369 km2 and have a volume of 54.2 km3 at a normal full-pool elevation of 

628.6 m. Excluding its outlet arm, the lake covers 329 

km2, contains 53.9 km3 , and is about 50 km in length.

Lake Pend Oreille, including its outlet arm, receives surface-water inflow from a 62,700-km2 drainage area, the vast majority of which is in northwestern 

Montana. About 85 percent of the lake's surface-water 

inflow is delivered by the Clark Fork (Frenzel, 1993a), 

which enters the lake from the east. The Clark Fork 

begins near Butte, Montana, and drains an extensive 

area west of the Continental Divide, including the Flathead River and Flathead Lake. The Clark Fork is 

impounded by Cabinet Gorge Dam about 11 km 

upstream from Lake Pend Oreille; the drainage area 

upstream from Cabinet Gorge Dam is 57,150 km2. The 

dam was completed in 1951 and is operated primarily 

for hydroelectric power generation. Lake Pend Oreille 

is drained by the Pend Oreille River, a tributary to the 

Columbia River.

Much of Lake Pend Oreille's drainage basin is 

characterized by mountainous terrain interspersed with 

broad valleys. Elevations range from about 3,000 m in 

northwestern Montana and Glacier National Park to 

about 600 m near the Idaho-Washington border. In the 

lake's southern basin, much of the shoreline rises precipitously to elevations between 1,500 and 2,000 m. 

Most land cover in the basin is coniferous forest; rangeland and agriculture together account for about 20 percent. Land-use activities include recreation, logging, 

agriculture, mining, and grazing; urban land use 

applies to only about 1 percent of the drainage area.

Lake Pend Oreille responds to a wide range of climatological conditions because the drainage area of the 

Clark Fork is so large relative to the lake's local drain8 Fate and Transport of Nitrogen and Phosphorus, Coeur d'Alene Lake, Lake Pend Oreille, and Flathead Lake
age area. Most of the annual precipitation is snow during the winter months. The influence of Pacific Maritime conditions can produce large rain-on-snow events 

during the winter. Mean annual precipitation at the 

northern end of the lake is 84 cm, whereas it is 125 cm 

in the adjacent mountains. Near the Continental Divide 

in northwestern Montana, mean annual precipitation is 

about 250 cm. Because of its considerable volume and 

heat-storage capacity, the lake does not freeze except at 

the shallow northern end.

Similar to Coeur d'Alene and Flathead Lakes, the 

potential for eutrophication by excessive nutrient loads 

is a water-quality concern for Lake Pend Oreille. Studies in the early 1990s documented that increased lake 

productivity was manifested largely in the littoral zone; 

the lake's limnetic zone remained oligotrophic (Hoelscher and others, 1993). The lake's primary inflow, the 

Clark Fork, contributed about 80 percent of the nitrogen and phosphorus loads annually delivered to the 

lake (Frenzel, 1993b). Trace-element contamination 

is another water-quality issue for Lake Pend Oreille. 

More than a century of mining, ore-processing, and 

tailings disposal has left the upper Clark Fork severely 

contaminated with trace elements (Andrews, 1987; 

Moore and Luoma, 1990); as a result, four Superfund 

sites have been listed in the upper Clark Fork. Several 

impoundments downstream from the Superfund sites 

and upstream from Lake Pend Oreille have trapped part 

of the trace-element-contaminated sediments introduced into the Clark Fork (Moore, 1997). However, 

bed-sediment samples collected from Lake Pend 

Oreille by the U.S. Army Corps of Engineers (PL. 

Hall, U.S. Army Corps of Engineers, written commun., 

1989) and collected in the Pend Oreille River near its 

confluence with the Priest River by the U.S. Geological 

Survey (Beckwith, 2002) indicated substantially elevated concentrations of cadmium, copper, lead, and 

zinc. These results suggest that trace-element-contaminated sediments are being transported into and through 

the lake.

EVALUATION APPROACH

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 within the 

lake over a wide range of spatial and temporal scales.

The outcome of those interactions determines the quantity and nature of constituents discharged from the lake 

at its surface-water outlet. Nitrogen and phosphorus 

compounds, the principal constituents of concern in 

this report, occur in dissolved, colloidal, and particulate 

fractions. These fractions of nitrogen and phosphorus 

vary in their degree of participation in chemical and 

biological processes within the lake's water column, as 

well as within the lakebed sediments. The lake's effect 

on fate and transport is likely to be quite different for 

particulate-fraction constituents, which have high densities relative to that of water, than for dissolved-fraction and colloidal-fraction constituents, which have low 

densities. In general, lakes are efficient traps for sediment because the significant decrease in flow velocity 

and turbulence within a lake inhibits advective transport of sediments and particulate-fraction constituents. 

In contrast, dissolved and colloidal constituents are 

transported by convection and diffusion, as well as by 

advection, after their delivery into a lake.

The initial phase of the evaluation was to quantify 

the differences in nutrient loadings upstream and downstream from each lake. The second phase was to define 

the combined influence of the hydrologic characteristics of each drainage basin and physical limnological 

characteristics of each lake on the fate and transport of 

nutrients. The third phase was to determine the spatial 

and temporal variability of chemical and biological 

constituents and partitioning of nutrients within each 

lake. The final phase was to combine the insight gained 

from the first three phases of evaluation to distinguish 

the effects of hydrological and physical limnological 

processes from the effects of chemical and biological 

processes in determining nutrient fate and transport 

through each lake's water mass.

NUTRIENT LOADS

Overview

The primary objective of quantifying nutrient 

loads in this evaluation was to demonstrate the importance of understanding how limnological processes 

influence the quantitative differences between loads of 

nutrients input to and output from a lake. The initial 

step in gaining this understanding is to quantify those 

nutrient loads over equivalent timescales. Load is defined as the quantity of a constituent passing a riverine

Nutrient Loads 9
cross section per unit of time and is calculated as the 

product of constituent concentration, discharge, and 

appropriate conversion factors for measurement units.

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. 

Both constituent concentration and discharge vary substantially over the course of a year. Perhaps more 

importantly, the two quantities are nonsynchronous in 

their temporal variation; also, concentrations of dissolved constituents respond differently to discharge 

changes than do concentrations of particulate constituents. Thus, constituent loads may vary on a daily, 

monthly, and (or) annual basis. A variety of methods, 

from basic to complex, have been used to process multiple-date data sets of concentration and discharge into 

estimates of seasonal and annual loads. A 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, both 

within and among years, because changes in discharge 

are often 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 sediment-associated constituents 

within a year typically are associated with minimum 

discharges, owing to reduced water velocities that produce less erosion and transport. Alternatively, elevated 

water velocities during maximum discharge within a 

year result in erosion and transport of the largest loads 

of sediment-associated constituents. The pattern is generally similar for dissolved constituents, but differences 

in loads between high and low discharge are reduced 

because the transport of dissolved constituents is less 

dependent on stream velocity. These within-year patterns of variability in loads for sediment-associated and 

dissolved constituents are important considerations in 

assessing a lake's effects on the fate and transport of 

nutrient loads. The foregoing logic for seasonal loads 

also applies to annual loads; in general, larger constituent loads are transported during high-discharge years 

than during low-discharge years.

A lake's hydrologic budget, an accounting of the 

amount of water entering and exiting the lake, is an 

important determinant of constituent loads delivered 

into and discharged from the lake. The hydrologic budget provides an accounting of gains and losses of water 

associated with surface-water inflow and outflow, precipitation and evaporation, ground-water inflow and 

outflow, wastewater-treatment facility inflows, industrial and municipal withdrawals, and changes in lake 

storage. If each water source for the lake can be quantified and assigned an associated concentration, then a 

constituent budget can be calculated for the lake. Hydrologic and constituent budgets are important tools for 

evaluating the in-lake fate and transport of particulate, 

colloidal, and dissolved constituents that affect lake 

water-quality characteristics.

Coeur d'Alene Lake

A nutrient load/lake response study of Coeur 

d'Alene Lake conducted cooperatively by the USGS 

and Idaho Department (formerly, Division) of Environmental Quality (IDEQ) quantified hydrologic, nutrient, 

and trace-element budgets for calendar years 1991 and 

1992 (Woods and Beckwith, 1997). Numerous budget 

components were quantified, either by measurement or 

estimation; details about data sources and computations were presented by Woods and Beckwith (1997). 

Riverine-derived constituent loads were computed 

using the computer program FLUX (Walker, 1996), a 

regression-based approach for estimating loads that 

stratifies streamflow and constituent concentration data 

to reduce prediction error. The stratified data sets then 

are used to compute a series of loads on the basis of 

five different regression equations. The regression 

equation and stratification method that yields the smallest coefficient of variation is considered the best estimate of load. FLUX provides several additional diagnostic tools for assessing results; these include plots of 

residuals and hypothesis tests for various model parameters.

The hydrologic budgets reported by Woods and 

Beckwith (1997) indicated that the combined inflows 

from the lake's two primary tributaries, the Coeur 

d'Alene and St. Joe Rivers, accounted for about 92 percent of all inflows to the lake. The St. Joe River was the 

larger inflow source, delivering about one-half of the 

inflow to the lake. Precipitation on the lake surface

10 Fate and Transport of Nitrogen and Phosphorus, Coeur d'Alene Lake, Lake Pend Oreille, and Flathead Lake
accounted for less than 2.5 percent of the hydrologic 

budget in each year. At least 90 percent of the water 

exiting the lake was by way of the Spokane River, the 

remainder was evaporation loss from the lake surface 

and ground-water outflow from the lake's northern 

margin.

Annual loads of total nitrogen and phosphorus 

delivered to and discharged from Coeur d'Alene Lake 

during 1991 and 1992 (table 1) were calculated on the 

basis of constituent budgets reported by Woods and 

Beckwith (1997). These 2 years represented different 

hydrologic conditions for the lake. In 1991, the annual 

mean lake outflow as measured in the Spokane River 

was 199 m3/s, or 112 percent of the long-term mean 

annual outflow of 177 m3/s (Brennan and others, 

2001); in contrast, annual mean lake outflow for the 

1992 water year was 99 m3/s, only 56 percent of the 

long-term value. As expected, nitrogen and phosphorus 

loads for 1992 were also substantially less than those 

for 1991. On the basis of magnitude, the St. Joe River, 

and then the Coeur d'Alene River, delivered the most 

nitrogen and phosphorus to the lake. Combined, these 

two rivers delivered 83 and 82 percent, respectively, of 

the total nitrogen and phosphorus loads during 1991- 

92. Atmospheric deposition of nutrients on the lake 

surface by precipitation and dryfall was minor, deliverTable 1 . Annual input, output, and retained loads of total 

nitrogen and phosphorus, Coeur d'Alene Lake, Idaho, 

calendar years 1991 and 1992

[kg, kilograms; km3, cubic kilometers; retained load values are rounded]

Variable, unit

Mean annual lake outflow2, km3

M991

6.37

M992

3.17

Total nitrogen

Input load, kg

Output load, kg

Retained load3 , kg

Retained load/input load, percent

2,150,000

2,030,000

120,000

6

945,000

860,000

85,000

9

Total phosphorus

Input load, kg

Output load, kg

Retained load3 , kg

Retained load/input load, percent

115,000

36,100

78,900

69

43,600

27,600

16,000

37

1 From Woods and Beckwith (1997).

2 Measured at Spokane River near Post Falls, Idaho (station 4, fig. 1).

3 Input load-output load.

ing less than 8 percent of the nitrogen and less than 

15 percent of the phosphorus.

The magnitude and percentage of the total nitrogen and phosphorus loads retained by the lake also 

were calculated on the basis of Woods' and Beckwith's 

1997 constituent budgets (table 1). The retained load 

of nitrogen was 85,000 kg in 1992, 35,000 kg less than 

in 1991. However, the retained loads for each year were 

a similar percentage of their respective input loads, 5.6 

percent in 1991 and 9.0 percent in 1992. The retained 

load of phosphorus in 1991 was 78,900 kg, about 5 

times that retained in 1992. Unlike nitrogen, the 

retained loads for phosphorus were not similar between 

the 2 years; the percentage in 1991 was 69 but, in 1992, 

the percentage was only 37. On this basis, the large differences in inflow and outflow volumes for 1991 and 

1992 had little effect on the lake's ability to retain 

nitrogen but a large effect on its ability to retain phosphorus.

Flathead Lake

The primary sources of hydrologic and nutrient 

budget information for Flathead Lake were twofold: a 

doctoral dissertation examining the effects of turbidity 

on the lake's biogeochemistry and trophic state (Stuart, 

1983), and a 1978-82 limnological assessment (Stanford and others, 1983) prepared for the U.S. Environmental Protection Agency (EPA). Numerous additional 

years of nutrient budget information for Flathead Lake 

also were presented by Stanford and others (1995, 

1997); however, much of their phosphorus load data 

could not be used for the purposes of this report because of an introduced bias. These authors adjusted 

their nutrient load calculations for phosphorus to focus 

on bioavailable (dissolved) phosphorus; when the total 

suspended-solids concentration in a sample exceeded 

10 mg/L, they reduced the associated total phosphorus 

concentration in that sample by 90 percent. The effect 

was to mathematically discount most of the sedimentassociated phosphorus load from the lake's primary 

inflow source, the Flathead River, and, thereby, bias the 

calculation of phosphorus retention in Flathead Lake.

The limnological assessment (Stanford and others, 

1983) presented hydrologic and nutrient budgets for 

1978-82, as well as details about data sources and 

computations for loads delivered from riverine, atmospheric, wastewater, and nearshore sources. Riverinederived constituent loads were computed using monthNutrient Loads 11
ly mean values of streamflow and nutrient concentration. The total phosphorus loads reported in the limnological assessment included the introduced bias described earlier, but the bias affected only the influent 

Flathead River because suspended-sediment concentrations at the lake's outlet did not exceed 10 mg/L. Fortunately, the authors reported both unbiased and biased 

total phosphorus loads for the Flathead River for 1978- 

82, thereby providing the data needed to calculate an 

unbiased total phosphorus budget for the lake over that 

period. The additional years of nutrient budgets reported by Stanford and others (1995, 1997) covered a 

wide range of hydrologic conditions; however, only 

biased phosphorus loads were reported.

Hydrologic and nutrient budgets calculated by 

Stanford and others (1983) for 1978-82 were reported 

as a mean for that period; these are summarized in 

table 2. Inflow from the Flathead River accounted

Table 2. Mean annual input, output, and retained loads of 

total nitrogen and phosphorus, Flathead Lake, Montana, 

1978-82

[kg, kilograms; km3 , cubic kilometers; mg/L, milligrams per liter]

Variable, unit

Mean annual lake outflow, km3

1 1978 -82

9.41

Total nitrogen

Input load, kg

Output load, kg

Retained load2, kg

Retained load/input load, percent

1,590,000

1,020,000

570,000

36

Total phosphorus, biased

Input load, kg

Output load, kg

Retained load2, kg

Retained load/input load, percent

118,000

59,300

58,700

50

Total phosphorus, unbiased 4

Input

Output

Retained load2, kg

Retained load/input load, percent

242,000

59,300

183,000

76

1 From Stanford and others (1983); loads converted from metric 

tons to kilograms.

"• Input load-output load.

- Concentrations reduced 90 percent if suspended-solids concentrations larger than 10 mg/L for Flathead River inflow.

Concentrations not reduced to account for suspended-solids concentrations larger than 10 mg/L for Flathead River inflow.

for 87 percent of the lake's hydrologic budget during 

1978-82; the Swan River (fig. 1) and direct precipitation on the lake surface accounted for most of the 

remaining inflow (Stuart, 1983). About one-half of 

the annual inflow to the lake was delivered during 

April to July, the period of snowmelt runoff (Stuart, 

1983). Regarding outflow from the lake, 97 percent 

was by way of the Flathead River, and 3 percent was 

evaporation loss from the lake surface (Stuart, 1983). 

Hydrologic conditions were slightly less than average; 

the mean annual lake outflow of 294 m3/s, as measured 

at Perma, during 1978-82 (table 2) was about 88 percent of the long-term mean of 336 m3/s (Shields and 

others, 2001). Similar to Coeur d'Alene Lake, the input 

and output loads of total nitrogen were much larger 

than those of total phosphorus (table 2). Details on the 

nitrogen budget reported by Stanford and others (1983) 

indicated that the Flathead River delivered 80 percent 

of the nitrogen load to the lake, and precipitation on the 

lake surface delivered 11 percent. For the biased total 

phosphorus loads to the lake (Stanford and others, 

1983), the Flathead River delivered 64 percent, 

whereas precipitation on the lake surface delivered 

25 percent. If unbiased total phosphorus inputs are 

used, the Flathead River delivered 82 percent of the 

lake's total phosphorus load; precipitation delivered 

12 percent.

During 1978-82, the retained load of nitrogen 

in Flathead Lake was 570,000 kg, or 36 percent of 

the input load (table 2). The biased retained load of 

phosphorus was 58,700 kg, or 50 percent of the input 

load; the unbiased retained load of phosphorus was 

183,000 kg, or 76 percent of the input load. Unlike 

the multiple-year data set available for Coeur d'Alene 

Lake, Flathead Lake lacks unbiased nutrient data for 

estimating the effects of streamflow on the magnitude 

of nutrient loads retained by the lake.

Lake Pend Oreille

As part of a nutrient load/lake response study 

of Lake Pend Oreille conducted cooperatively by the 

USGS and IDEQ, hydrologic and nutrient budgets for 

numerous sources were quantified for water years 1989 

and 1990 (Frenzel, 1993a,b). Riverine-derived nutrient 

loads were computed using the same computer program, FLUX (Walker, 1996), that was used for the 

nutrient load/lake response study of Coeur d'Alene 

Lake (Woods and Beckwith, 1997). Hydrologic bud12 Fate and Transport of Nitrogen and Phosphorus, Coeur d'Alene Lake, Lake Pend Oreille, and Flathead Lake
gets reported by Frenzel (1993 a) indicated that the 

inflow from the lake's primary tributary, the Clark 

Fork, accounted for about 85 percent of all inflows to 

the lake and its outlet arm. The Priest River (fig. 1), 

located near the downstream end of the lake's outlet 

arm, accounted for 6.4 percent of inflow to the lake and 

its outlet arm. Precipitation on the lake and outlet arm 

surface accounted for about 1.3 percent of the hydrologic budget in both years. At least 98 percent of the 

water discharged from the lake was by way of the Pend 

Oreille River; much of the remainder was evaporation 

loss from the lake surface.

Annual loads of total nitrogen and phosphorus 

delivered to and discharged from Lake Pend Oreille, 

including its outlet arm, during 1989 and 1990 (table 3) 

were calculated on the basis of the constituent budgets 

reported by Frenzel (1993b). In 1989, the annual 

mean lake outflow of 627 m3/s was 88 percent of the 

long-term mean annual outflow of 716 m3/s (Brennan 

and others, 2001); the annual mean lake outflow of 

799 m3/s in 1990 was 112 percent of the long-term 

value. Nitrogen and phosphorus loads for the aboveaverage outflow year, 1990, were larger than those for 

1989, thereby illustrating the strong positive correlation 

between load and streamflow. In both years, the Clark 

Fork delivered about 80 percent of the lake's nitrogen 

load and about 70 percent of its phosphorus load (Frenzel, 1993b). The Priest River delivered about 6 percent 

of the nitrogen load and about 9 percent of the phosphorus load. Atmospheric deposition delivered about 

4.3 percent of the nitrogen load and about 5.8 percent 

of the phosphorus load in both years.

The retained load of nitrogen in Lake Pend Oreille 

was 670,000 kg in 1989 and 840,000 kg in 1990 

(table 3). Despite a substantial difference in outflow 

volumes, the retained loads were similar percentages 

of the input load, 15.2 in 1989 and 14.8 percent in 

1990. Retained loads of phosphorus also were similar 

percentages of the input load, 16.9 in 1989 and 13.5 in 

1990. On this basis, the large difference in the lake's 

hydrologic budgets for 1989 and 1990 had little effect 

on the percentages of nitrogen and phosphorus loads 

retained by the lake.

Table 3. Annual input, output, and retained loads of total 

nitrogen and phosphorus, Lake Pend Oreille, Idaho, water 

years 1989 and 1990

[kg, kilograms; km3, cubic kilometers]

Variable, unit

Mean annual lake outflow2, km3

1989

20.0

!1990

25.6

Total nitrogen

Input load, kg

Output load, kg

Retained load3 , kg

Retained load/input load, percent

4,410,000

3,740,000

670,000

15

5,670,000

4,830,000

840,000

15

Total phosphorus

Input load, kg

Output load, kg

Retained load3 , kg

Retained load/input load, percent

326,000

271,000

55,000

17

408,000

353,000

55,000

14

1 From Frenzel (1993b).

2 Measured at Pend Oreille River at Newport, Wash, (station 7, fig. 1).

3 Input load-output load.

Among-Lake Comparisons

The annual loads of nutrients delivered to the three 

lakes varied widely; total nitrogen loads ranged from 

945,000 to 5,670,000 kg, whereas total phosphorus 

loads ranged from 43,600 to 408,000 kg (tables 1-3). 

Lake Pend Oreille received the largest loads of both 

nutrients; Coeur d'Alene Lake received the smallest. 

Nutrient loads discharged from the lakes ranged from 

860,000 to 4,830,000 kg of total nitrogen and from 

27,600 to 353,000 kg of total phosphorus (tables 1-3). 

Similar to input loads, Lake Pend Oreille discharged 

the largest loads of both nutrients and Coeur d'Alene 

Lake discharged the smallest.

The variable, retained load/input load (tables 1 -3), 

was averaged for total nitrogen and phosphorus 

(table 4). Coeur d'Alene Lake retained the smallest 

percentage (7.3) of nitrogen and Flathead Lake retained the largest percentage (36). On the basis of unbiased loads, Lake Pend Oreille retained the smallest 

percentage (15) of phosphorus, Coeur d'Alene Lake 

retained 53 percent, and Flathead Lake retained the 

largest percentage (76).

Nutrient Loads 13
Table 4. Average of retained load/input load for total nitrogen 

and phosphorus, Coeur d'Alene Lake and Lake Pend Oreille, 

Idaho, and Flathead Lake, Montana

Lake

Coeur d'Alene 2 ....

Flathead3 .........

Pend Oreille 5 ......

Average retained load '/ input load, 

in percent

Total nitrogen

7.3

36

15

Total phosphorus

53

4 76

15

1 Input load - output load.

2 Based on calendar years 1991-92, see table 1.

3 Based on calendar years 1978-82, see table 2.

4 Unbiased loads from Flathead River.

5 Based on water years 1989-90, see table 3.

PHYSICAL LIMNOLOGY

Overview

The initial phase of evaluation demonstrated substantial quantitative differences in the relative amounts 

of nutrient loads delivered to and discharged from the 

three lakes. The next phase, discussed in this section, 

defines the quantitative differences in light of the combined influence of the hydrologic characteristics of 

each drainage basin and physical limnological characteristics of each lake.

One measure of the potential influence of a drainage basin on a lake is the ratio of drainage basin area to 

lake surface area. As that ratio increases, a concomitant 

increase in the hydrologic influence of the drainage 

basin upon the lake receiving the basin's runoff might 

be expected. However, two problems arise in this comparison of surface areas: (1) runoff from a drainage 

basin is highly dependent upon the amount of precipitation it receives, and (2) lake surface area is a poor 

indicator of lake volume. Calculation of areal water 

load deals more effectively with the issue of drainage 

basin area because the volume of runoff delivered into 

the lake is divided by lake surface area. As areal water 

load increases, the drainage basin's hydrologic influence on the lake also increases. The second problem, 

lake surface area, can be dealt with by considering the 

ratio of inflow volume to lake volume, commonly 

termed flushing rate (Ryding and Rast, 1989). As 

flushing rate increases, the drainage basin's hydrologic

influence on the lake also increases because the lake's 

volume is replaced more frequently. The inverse of 

flushing rate is termed retention time and represents the 

time theoretically needed to fill a lake if it were empty. 

If lake volume is divided by lake outflow volume instead of inflow volume, then the time needed to empty 

the lake, the hydraulic residence time, is obtained. On 

an annual basis, retention time and hydraulic residence 

time often are comparable. Hydraulic residence time 

was chosen for analysis in this report because outflow 

volumes for the three lakes have been measured for 

many years.

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. The rate at which 

water enters and leaves a lake affects the amount of turbulence within the lake's water column, both in the 

horizontal and vertical dimensions. Years of above-normal inflow and outflow produce more water-column 

turbulence and increase advective transport of particulate materials. Conversely, years of below-normal inflow and outflow produce less water-column mixing 

and, hence, increase the trapping of sediment and associated constituents.

The potential for trapping of sediment by water 

bodies such as lakes and reservoirs can be estimated 

empirically on the basis of a nomograph that relates the 

ratio of storage capacity (lake volume) to inflow volume (Gray, 1973). That ratio is analogous to retention 

time. In the case of these three lakes, outflow volume 

was substituted for inflow volume; as such, hydraulic 

residence time was used in the nomograph to estimate 

trap efficiency. Given a hydraulic residence time of 

0.01 year (for example, a 25-km3 volume with a 2,500- 

km3 -per-year outflow volume), the estimated trap efficiency for sediment from the nomograph would be 

about 45 percent. If the hydraulic residence time were 

increased to 0.1 year (for example, a 25-km3 lake volume with a 250-km3 -per-year outflow volume), the 

estimated trap efficiency would be about 86 percent. 

The estimated trap efficiency would increase to 95 percent or greater for hydraulic residence times equal to or 

longer than 1.0 year (for example, a 25-km3 lake volume with a 25-km3 -per-year outflow volume).

The foregoing discussion provides insight into the 

relation of inflow or outflow magnitude on the generation of turbulence and advective transport within lakes. 

However, the concepts of retention and hydraulic residence times remain theoretical because lakes rarely are

14 Fate and Transport of Nitrogen and Phosphorus, Coeur d'Alene Lake, Lake Pend Oreille, and Flathead Lake
filled or emptied; the two descriptors are best suited for 

general comparisons among lakes representing wide 

ranges of retention and hydraulic residence times. In 

actuality, the movement of riverine inflows within a 

lake can be quite complex because of characteristics 

such as lake shape, lake depth, and temporal and spatial 

differences in density between riverine and lake water. 

Three generalized cases of inflow-plume routing were 

discussed by Fischer and others (1979): overflow, interflow, and underflow. Overflow occurs if the inflow 

plume is warmer (less dense) than the lake; river water 

floats on the lake's surface. Interflow occurs when the 

inflow plume is colder than the lake's upper water column but warmer than the lower water column; thus, 

interflow is routed to the lake depth where the temperature, or density, of the inflow plume and lake is equal. 

Underflow occurs when the inflow plume is colder 

than, or about the temperature of, the lake's 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 turbulence 

and advective transport.

The physical, chemical, and biological responses 

of a lake to the delivery of water and associated constituents from its drainage basin are closely tied to morphometric characteristics of the lake. Calculation of 

such characteristics requires a bathymetric map of the 

lake; such maps are available for Coeur d'Alene Lake 

(Woods and Berenbrock, 1994), Flathead Lake (Stanford and others, 1997), and Lake Pend Oreille (Fields 

and others, 1996). Lake shape can vary from circular 

to elongate to dendritic. A long, narrow lake such as 

Coeur d'Alene Lake is more prone to channel inflow 

along its major axis. Flathead Lake and Lake Pend 

Oreille are also long but are much wider than Coeur 

d'Alene Lake; hence, their inflows are less prone to 

channeling along their major axis. Surface area affects 

the amount of atmospheric materials that may be 

directly deposited onto the lake's surface versus those 

deposited onto the lake's drainage basin. Surface area 

and lake shape are determinants of the lake's exposure 

to wind. A large surface area in combination with long 

or wide reaches increases the wind's ability to generate 

turbulence and mix the lake's water column. The maximum length and maximum width of a lake are useful

descriptors of this effect but fail to convey the sheltering effects of islands or the shoreline. Maximum effective length and maximum effective width (Hakanson, 

1981) are better indicators of wind exposure because 

they represent linear reaches absent from wind sheltering. Increased wind exposure favors the development 

of large-scale turbulent processes such as surface and 

internal seiches, which can displace large masses of 

water in the horizontal and vertical dimensions and, 

thus, are important mechanisms for water-column 

mixing.

Depth is also a critical lake dimension for several 

reasons. Deep lakes are more resistant to turbulent, 

full-depth mixing by wind energy, so lakebed sediments are less likely to be periodically resuspended. 

Because of longer settling time, organic detritus in a 

deep lake is more likely to have undergone remineralization by the time it reaches the lakebed. 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. Maximum depth only conveys information about the deepest part of a lake. The mean depth, 

defined as lake volume divided by lake surface area, 

provides more information about the distribution of 

depth throughout a lake. A lake with a large surface 

area and extensive shallow areas has a relatively small 

mean depth because of its small volume. A similarsized lake with extensive deep areas has a larger mean 

depth because of its large volume. For large lakes, 

mean depth is considered the primary morphometric 

variable because of its general inverse correlation with 

lake productivity (Wetzel, 1975). Mean depth also has 

been an important variable in the development of 

empirical models relating lake productivity to nutrient 

loadings (Reckhow and Chapra, 1983).

The vertical distribution of water-quality properties and constituents are closely linked to the physical 

limnological processes of thermal stratification and 

convective circulation. Thermal structure in some lakes 

may be established, in part, by riverine inflows routed 

as overflow. However, the major source of heat for 

most lakes is the solar radiation that impinges upon the 

lake's surface (Wetzel, 1975). 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

Physical Limnology 15
epilimnion, is the stratum in which most of the lake's 

biological production occurs because light is generally 

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 l°C/m. The hypolimnion overlies 

the lakebed sediments and typically has more thermal 

stability than the epilimnion and metalimnion do. During thermal 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 the spring and autumn, solar radiation is less 

than during the summer, and windy conditions also 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 in the spring and autumn. Such mixing is 

an important mechanism for the vertical movement of 

water-quality constituents such as dissolved oxygen, 

nutrients, and trace elements.

Among-Lake Comparisons

The three lakes differ widely in many of their 

physical limnological characteristics, as shown in 

table 5. The drainage areas of Coeur d'Alene and Flathead Lakes are comparable; that of Lake Pend Oreille 

is about 6 times larger. Coeur d'Alene Lake has a surface area about 4 times smaller than Flathead Lake's; 

the surface area of Lake Pend Oreille is about midway 

between that of the other two lakes. These areal differences yield ratios of drainage area to lake surface area 

of 23 for Flathead Lake, 75 for Coeur d'Alene Lake, 

and 190 for Lake Pend Oreille. On the basis of this 

ratio alone, Flathead Lake is expected to be the least 

affected by its drainage basin and Lake Pend Oreille to 

be the most affected. A similar conclusion results from 

comparison of areal water loads for the three lakes. 

Owing to the large surface area of Flathead Lake, the 

lake's mean annual outflow volume yields the smallest 

areal water load of the three lakes. The large mean

annual outflow volume for Lake Pend Oreille, coupled 

with its intermediate surface area, yields the largest 

areal water load.

When mean annual outflow volume and lake volume are considered together and expressed as hydraulic 

residence time, a more realistic appraisal of the hydrologic effects of the drainage basins on physical mixing 

processes within the three lakes is obtained. Lake volumes range from 2.8 (Coeur d'Alene Lake) to 53.9 km3 

(Lake Pend Oreille), as shown in table 5. Coeur 

d'Alene Lake also has the shortest hydraulic 

residence time, 0.50 year, and so by this measure is 

expected to be the most rapidly affected by runoff from 

its drainage basin. The other two lakes have longer and 

comparable hydraulic residence times; 2.2 years for 

Flathead Lake and 2.4 years for Lake Pend Oreille. 

Although Lake Pend Oreille has about twice the volume of Flathead Lake, it also has about twice the mean 

annual outflow volume. To put these values in perspecTable 5. Physical limnological characteristics, Coeur d'Alene 

Lake and Lake Pend Oreille, Idaho, and Flathead Lake, 

Montana

[km2, square kilometers; m, meters; km, kilometers; km3 , cubic kilometers; 

m/yr, meters per year; yr, year]

Characteristic, unit

Drainage area at outlet, km2

Lake surface elevation2, m

Surface area2, km2

Maximum length, km

Maximum effective length, km

Maximum width, km

Maximum effective width, km

Volume 2, km3

Maximum depth 2, m

Mean depth 2, m

Drainage area: surface area, unitless

Mean annual outflow volume, km3

Areal water load 3 , m/yr

Hydraulic residence time 3 , yr

Trap efficiency 3 , percent

Coeur 

d'Alene

9,690

648.7

129

35

12.5

3.7

3.7

2.8

63.7

21.7

75

5.6

43.2

.50

93

Flathead

11,400

879

496

56

56

26

18.5

23.2

113

50.2

23

10.6

21.4

2.2

97

Pend 

Oreille 1

62,700

628.6

329

50

21

10.8

10.8

53.9

357

164

190

22.6

68.6

2.4

98

1 Exclusive of Pend Oreille River outlet arm, which starts at Sandpoint, Idaho.

2 At normal full pool.

3 At mean annual outflow volume.

16 Fate and Transport of Nitrogen and Phosphorus, Coeur d'Alene Lake, Lake Pend Oreille, and Flathead Lake
tive, note that hydraulic residence times (equivalently, 

retention times) may be on the order of days for rapidly 

flushed, run-of-the-river reservoirs to hundreds of years 

for large-volume lakes with relatively small drainage 

basins. Examples of the latter are Crater Lake, Oregon, 

with a retention time of about 150 years, and Lake 

Tahoe, California/Nevada, with a retention time of 

about 700 years.

The trap efficiency for sediment delivered to these 

three lakes was estimated empirically by applying their 

hydraulic residence times to the previously discussed 

nomograph presented by Gray (1973). As listed in 

table 5, trap efficiencies for the three lakes exceed 

90 percent. Coeur d'Alene Lake has the smallest, 

93 percent; the other two lakes can be expected to trap 

more than 97 percent of the sediment loads delivered to 

them.

Morphometric features for the three lakes are illustrated in bathymetric maps (figs. 2-4) and described in 

table 5. None of these lakes approaches a round shape, 

but Coeur d'Alene Lake is the smallest in width and 

length (3.7 and 35 km, respectively); Flathead Lake is 

the largest (26 and 56 km, respectively); and Lake Pend 

Oreille is intermediate (10.8 and 50 km, respectively). 

The degree of lake surface exposure to wind can be 

judged on the basis of maximum effective widths and 

lengths. Coeur d'Alene Lake has the smallest dimensions for these two variables, 3.7 and 12.5 km, respectively. Flathead Lake's maximum effective width is 

about 70 percent of its maximum width, but its maximum effective length and maximum length are equal 

(56 km). Lake Pend Oreille's maximum effective width 

and maximum width are also equal (10.8 km); however, its maximum effective length is less than half of 

its maximum length. Given equivalent wind conditions, 

Flathead Lake is most exposed to wind over both width 

and length; Coeur d'Alene Lake is least exposed in 

both dimensions.

Bathymetric contours of the three lakes (figs. 2-4, 

table 5) illustrate Lake Pend Oreille as the deepest; it is 

more than 3 times deeper than Flathead Lake and about 

5.5 times deeper than Coeur d'Alene Lake. Lake Pend 

Oreille also has the largest mean depth (164 m), whereas Coeur d'Alene Lake has the smallest (21.7 m). Owing to its large mean depth and intermediate-sized surface area, Lake Pend Oreille has the largest volume 

(53.9 km3 ) of the three lakes. Woods (1993b) calculated that about 95 percent of Lake Pend Oreille's volume is contained in the deep southern basin, south of 

the northernmost extent of depths greater than 200 m

(fig. 4). Although not uniform, the variation of depth in 

the other two lakes is less dramatic than in Lake Pend 

Oreille (figs. 2 and 3).

The foregoing section presented morphometric 

characteristics that indicate the extent to which runoff 

from the drainage basin or wind-induced mixing can 

produce varying degrees of water-column turbulence 

among the three lakes. These morphometric characteristics are fairly general and easily derived from bathymetric maps and annual discharge data. The next three 

sections present additional data to evaluate in more 

detail how water-column turbulence in each lake is 

affected by interannual (among multiple years) and 

intraannual (within each year) variations in hydraulic 

residence time, inflow-plume routing, thermal stratification, and convective turnover.

Coeur d'Alene Lake

The hydraulic residence time of 0.50 year for 

Coeur d'Alene Lake (table 5) is based on a normal fullpool volume of 2.8 km3 divided by the mean annual 

outflow volume of 5.6 km3 . The lake's outflow volume 

statistics were derived for an 87-year period of record 

(1913-2000) for the USGS gaging station Spokane 

River near Post Falls, Idaho (station 4, fig. 1) (Brennan 

and others, 2001). Over that period of record, however, 

annual mean outflow volume has varied widely. For the 

minimum outflow volume of 1.9 km3 , the hydraulic 

residence time increases to 1.5 years; conversely, for 

the maximum outflow volume of 10.5 km3 , hydraulic 

residence time decreases to 0.27 year. This range of 

hydraulic residence times indicates that, in the absence 

of any inflow, the lake theoretically could drain 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 its presumed relation with hydraulic residence time. Coeur d'Alene 

Lake's ability to retain constituents delivered from its 

drainage basin is expected to decline as hydraulic residence time declines.

In addition to interannual variability, outflow from 

the lake varies intraannually in response to climatological conditions within its drainage basin. Over the 

1913-2000 period of record, the smallest monthly 

mean outflow of 0.07 km3 occurs in August, whereas 

the largest monthly mean outflow of 1.3 km3 occurs in 

May. On the basis of these outflow volumes, constituPhysical Limnology 17
Coeur

d'Alene

Lake

Spokane River 

outflow

Line of equal depth below 

lake surface at a normal 

full-pool elevation of 648.7 

meters. Contour interval 

10 meters. Datum is 

National Geodetic Vertical 

Datum of 1929

A Limnological station and 

3 number

Base from U.S. Geological Survey 

Benewah Lake, 1981; Black Lake, 1981; 

Chatcolet, 1981; Coeur d'Alene, 1981; 

Fernan Lake, 1981; Harrison, 1981; 

Mica Bay, 1981; Mt. Coeur d'Alene, 1981; 

Post Falls, 1981; Worley, 1981; 1:24,000 

Universal Transverse Mercator (UTM) 

projection. Zone 11

5 KILOMETERS

Figure 2. Bathymetry and locations of selected limnological stations, Coeur d'Alene Lake, Idaho.

18 Fate and Transport of Nitrogen and Phosphorus, Coeur d'Alene Lake, Lake Pend Oreille, and Flathead Lake
Flathead 

Lake

A 

3

EXPLANATION

Line of equal depth below lake 

surface at a normal full-pool 

elevation of 879 meters. 

Contour interval is variable. 

Datum is National Geodetic 

Vertical Datum of 1929

Limnological station and 

number

Contours from Stanford and others (1997)

Base from U.S. Geological Survey, 1:24,000 

Universal Transverse Mercator 

(UTM) projection. Zone 12

Flathead 

River 

inflow

012345678 9 KILOMETERS

I II III II I I

0 1 5 MILES Flathead

River

outflow

48 00'

47 52' 30"

47° 45'

Figure 3. Bathymetry and locations of selected limnological stations, Flathead Lake, Montana.

Physical Limnology 19
116° 30'

Lake

Pend

Oreille

48° 10'

Clark Fork 

inflow

Pend Oreille River

(Outlet arm of 

Lake Pend Oreille)

Line of equal depth below lake 

surface at a normal full-pool 

elevation of 628.6 meters. 

Contour interval 50 meters. 

Datum is National Geodetic 

Vertical Datum of 1929

Approximate boundary separating northern and southern 

basins of Lake Pend Oreille

Limnological station and 

number

Lake

Pend

Oreille

o 1 6 KILOMETERS

4 MILES

116° 30'

Base from U.S. Geological Survey

Bayview, 1967; Clark Fork, 1989; Cocolalla, 1968;

Hope, 1989; Lakeview, 1961; Minerva Peak, 1989;

Oden Bay, 1989; Packsaddle Mtn., 1989; Sandpoint,

1968;Talache, 1989; Trout Peak, 1989; 1:24,000

Universal Transverse Mercator (UTM) projection. Zone 11

Figure 4. Bathymetry and locations of selected limnological stations. Lake Pend Oreille, Idaho.

20 Fate and Transport of Nitrogen and Phosphorus, Coeur d'Alene Lake, Lake Pend Oreille, and Flathead Lake
ents delivered to the lake by way of inflow more likely 

would be retained in August when water-column turbulence is least.

The fate and transport of nutrients in Coeur 

d'Alene Lake are highly dependent upon inflow-plume 

routing of the lake's two primary inflow sources, the 

Coeur d'Alene and St. Joe Rivers. Inflow-plume routing was evaluated using water-temperature data from 

two limnological studies of Coeur d'Alene Lake conducted in the 1990s. Water-temperature data for the two 

rivers and numerous full-depth profiles of water temperature collected for most months during 1991-92 at 

six limnological stations (fig. 2) were reported by 

Woods and Beckwith (1997). The 1999 water year also 

was evaluated using similar water-temperature data; 

however, lake water-column sampling was conducted 

only during June through October at limnological stations 1, 3, 4, and 5 (fig. 2) (URS Greiner Inc., and 

CH2M-Hill Inc., 2001b). The 44 comparisons of 

inflow and lake temperatures reported for 1991-92 and 

1999 indicated that overflow was the most common 

mode of inflow-plume routing in about 60 percent of 

the comparisons (URS Greiner Inc., and CH2M-Hill 

Inc., 200Ib). Interflow or underflow was identified 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 the spring or autumn when the 

lake was most likely to be transitioning into or out of 

thermal stratification. Inflow volume also was evaluated as part of the 44 comparisons because it affects the 

spatial extent of inflow-plume routing. At small 

inflows, the plume's influence on the lake is reduced by 

rapid mixing and equilibration of riverine and lake temperatures; the converse is true for large inflows. Underflows tended to be associated only with small inflows, 

typical for the period 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 heat. Overflows occurred over a wide 

range of inflows because both the Coeur d'Alene and 

St. Joe Rivers have lengthy backwater-affected reaches 

that produce heating of inflow water by solar radiation.

The extent of inflow-plume routing into Coeur 

d'Alene Lake during the 1990s also was evaluated 

using unpublished information and several data sets not 

used in the foregoing analysis. A powerful storm during February 1996 dropped several inches of rain on a

substantial snowpack and created severe flooding in 

northern Idaho river basins, including the Coeur 

d'Alene and St. Joe River Basins. This storm delivered 

a large volume of sediment to Coeur d'Alene Lake and 

produced visible turbidity throughout the lake for several months (G.F. Harvey, Idaho Department of Environmental Quality, written commun., 2000). The magnitude of the February 1996 flood peaks at four longterm USGS gaging stations in the Coeur d'Alene and 

St. Joe River Basins was within about 10 percent of the 

100-year flood peak, on the basis of data reported by 

Beckwith and others (1996). On February 10,1996, the 

suspended-sediment concentration in the Coeur 

d'Alene River near its point of inflow to the lake 

(USGS gaging station Coeur d'Alene River near Hamson, Idaho, station 3, fig. 1) was 620 mg/L (Beckwith, 

1996) and was associated with a mean daily discharge 

of 1,550 m3/s. In comparison, the median and range of 

suspended-sediment concentrations in nine samples 

collected at the Harrison station during the 1999 water 

year were, respectively, 3.7 mg/L and 1.5 to 56 mg/L 

(A.J. Horowitz, U.S. Geological Survey, written commun., 1999); the latter concentration was associated 

with a mean daily discharge of 350 m3/s.

Inflow-plume routing into the lake also was evaluated using data collected during snowmelt runoff in the 

1997 water year. Changes in water-temperature profiles 

and water-column transparency (G.F. Harvey, Idaho 

Department of Environmental Quality, written commun., 2000) tracked the movement of the inflow plume 

into and through Coeur d'Alene Lake during May and 

June 1997. The temperature of the inflow plume on 

June 6, 1997, was 11°C, as measured at Coeur d'Alene 

River near Harrison (station 3, fig. 1) (Brennan and 

others, 1998). Water-column temperature profiles 

recorded on May 28 at four lake stations indicated the 

inflow plume was routed as a combination of overflow 

and interflow within the upper 10 m of the water column. Water-column transparencies, as measured by 

secchi disc on May 28, at the central and northern lake 

stations (stations 3 and 1, respectively, fig. 2) were 1.1 

and 2.0 m, respectively. By comparison, annual mean 

water-column transparencies at all four stations during 

1995 through 1999 ranged from 8 to 9 m (G.F. Harvey, 

Idaho Department of Environmental Quality, written 

commun., 2000).

Water-quality data from these large-volume discharge events of 1996 and 1997 revealed the routing of 

intact riverine inflows into and through Coeur d'Alene 

Lake; these inflows had been considered infrequent and

Physical Limnology 21
exceptional hydrologic events in which the lake acted 

as a conduit for the transport of constituents from the 

Coeur d'Alene and St. Joe Rivers to the Spokane River. 

However, this conceptual model was invalidated by the 

results of a limnological study, described in the following paragraph, of inflow-plume routing conducted during snowmelt runoff in the 1999 water year.

Discharge and chemistry of the Coeur d'Alene 

and St. Joe River inflow plumes into and through Coeur 

d'Alene Lake were tracked by USGS scientists using 

specialized water-quality instrumentation and watercolumn sampling. The short-term study sought to 

answer two questions: (1) can the riverine inflows and 

their associated chemical nature be clearly identified 

within the lake? and (2) do sediment, nutrients, and 

trace elements carried by the 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 and 3, 1999, at limnological stations 1 

through 5, in addition to three stations at the mouths of 

the Coeur d'Alene and St. Joe Rivers and at the lake's 

outlet into the Spokane River (fig. 2). The study results, 

reported in URS Greiner Inc., and CH2M-HU1 Inc. 

(200 Ib), clearly identified the riverine inflows as a 

combination of overflow and interflow within the upper 

5 to 13 m of the lake, from limnological station 4 and 

northward to the lake's outlet. Much of the lake south 

of limnological station 4 is shallow enough to allow 

full-depth mixing of the two riverine inflows. Only 

marginal influence from Coeur d'Alene and St. Joe 

River inflows was measured at limnological station 2, 

which is somewhat isolated from the northward flow of 

the two rivers. 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 larger than those in lake water. Zinc concentrations, also delivered almost exclusively by the 

Coeur d'Alene River, were smaller than those in lake 

water. Light transmission, conductivity, and nitrogen 

concentrations in riverine water also were smaller than 

those in lake water. The chemical nature of water exiting the lake to the Spokane River was more closely 

related to riverine inflows than to lake water. The 

January 1999 transport of sediment, nutrients, and trace 

elements through Coeur d'Alene Lake and into the 

Spokane River was measured during a snowmelt runoff 

event that occurs about every other year, on the basis of

long-term streamflow records for the USGS gaging station Coeur d'Alene River at Cataldo (station 2, fig. 1) 

(Kjelstrom and others, 1996).

The extent of thermal stratification and convective 

circulation in Coeur d'Alene Lake was evaluated on the 

basis of isopleth diagrams of water temperature reported for 1991-92 at six limnological stations (fig. 2) by 

Woods and Beckwith (1997) and water-temperature 

profiles measured during 1995-99 at limnological stations 1,3, and 4 (G.F. Harvey, Idaho Department of 

Environmental Quality, written commun., 2000). The 

lake was thermally stratified during 1991-92, commonly between early June and mid-November. Stratification developed in early June from a combination of 

solar heating of the lake's upper water column and riverine inflows from the Coeur d'Alene and St. Joe Rivers (URS Greiner Inc., and CH2M-Hill Inc., 200Ib). 

Those riverine inflows were delivered into the lake as 

overflows because both rivers have lengthy, backwateraffected lower reaches that facilitate heating by solar 

radiation. During 1991, thermoclines had developed by 

mid-July and persisted until early October; thermoclines again developed in 1992 from mid-June until 

early October. Although thermoclines were lost in early 

October, the lake remained thermally stratified into 

mid-November. The maximum thermocline depth was 

16.5 m in 1991 and 21.5 m in 1992. Similarly, maximum thermocline depths during 1995-99 ranged from 

15 to 24 m; their duration could not be determined 

because water-column profiles typically were measured during July through October and, thus, did not 

encompass the temporal extent of thermal stratification. 

Over those 7 years (1991-92, 1995-99), and when 

thermoclines were present, the epilimnion depth averaged about 10 m during July through September; this 

represents about 38 percent of the lake's total volume, 

on the basis of the depth-to-volume curve presented by 

Woods and Berenbrock (1994). The upper depth limit 

of the hypolimnion over the same period averaged 15 

m; thus, the hypolimnion constituted about 50 percent 

of the total lake volume. The remaining 12 percent of 

lake volume constituted the metalimnion during July 

through September. Coeur d'Alene Lake is dimictic in 

that it undergoes convective circulation twice a year. 

Spring circulation during 1991-92 was in April; the 

fall circulation was in late November of both years. The 

incidence of spring and fall circulation during 1995-99 

could not be evaluated.

22 Fate and Transport of Nitrogen and Phosphorus, Coeur d'Alene Lake, Lake Pend Oreille, and Flathead Lake
Flathead Lake

The hydraulic residence time for Flathead Lake is 

2.2 years (table 5), or about 4 times longer than for 

Coeur d'Alene Lake. That value is based on a normal 

full-pool volume of 23.2 km3 divided by the mean 

annual outflow volume of 10.6 km3 . The lake's outflow 

volume statistics were derived for a period of record 

from 1984 to 2000 for the USGS gaging station Flathead River at Perma, Montana (station 1, fig. 1) 

(Shields and others, 2001). The range in hydraulic residence time for this period was between 2.9 years, based 

on the minimum mean annual outflow of 7.9 km3 , and 

1.4 years, based on the maximum mean annual outflow 

of 16.1 km3 . The variation in outflow volume within a 

year was evaluated on the basis of minimum and maximum values for monthly mean outflow volume. For the 

1984-2000 period of record, the mean minimum outflow volume of 0.63 km3 was in August, whereas the 

mean maximum outflow volume of 1.7 km3 was in 

June. On the basis of these monthly mean outflow volumes, constituents delivered into the Flathead Lake by 

inflow would more likely be retained in August because of reduced water-column turbulence.

In-lake routing of the Flathead River's inflow 

within Flathead Lake was reported to occur as overflow 

during snowmelt runoff during 1978-80 (Stuart, 1983) 

and during 1983 (Stanford and others, 1983). The presence of overflow was determined from water-column 

profiles of percent light transmission (expressed as turbidity), spatial changes in transparency, and the lake's 

thermal structure in relation to the temperature of the 

influent Flathead River. The vertical extent of the 

plume ranged from the lake surface to between 10 and 

50 m in 1979 (Stuart, 1983). The augmentation of limnological sampling with aerial photography permitted 

evaluation of the advective transport of the plume within the lake; two generalized patterns emerged from this 

evaluation. In 1979, the plume (10°C) entered the lake 

(4°C) in early May and traveled directly south; by late 

June, the plume had spread throughout the lake. The 

second pattern, observed in 1980 and 1983, was more 

complicated. After entering the lake, the plume was 

deflected along the western shore until it met the constriction formed by the lake's shallow southern basin 

(fig. 3). From there, the plume split; part traveled south 

toward the lake's outlet, and the rest traveled northward 

along the lake's eastern shore. Stanford and others 

(1983) also noted an instance in which strong, westerly 

winds pushed the plume away from the western shore

and toward the middle of the lake. The dynamics of 

inflow-plume routing in Flathead Lake have been 

ascribed by Stanford and others (1983) to the following 

five principal factors: (1) natural flowpath of the Flathead River from north to south, (2) magnitude of snowmelt runoff, (3) density differences between influent 

Flathead River and the lake's thermal structure,

(4) Coriolis effect owing to the Earth's rotation, and

(5) co-occurrence of "thermal bars" adjacent to the 

littoral area of the lake during snowmelt runoff.

Patterns of thermal stratification and convective 

circulation in Flathead Lake were evaluated (Stanford 

and others, 1983) on the basis of isopleth diagrams of 

water temperature reported for 1978-79 at limnological station 2 (fig. 3). Additionally, the spatial similarity 

in thermal stratification among seven limnological stations was verified using selected temperature profiles 

from September 1991 through August 1993 (Stanford 

and others, 1994). Flathead Lake was thermally stratified between June and late October during 1978-79; 

thermocline depths ranged from about 8 to 15m. Thermal stratification developed largely from solar heating 

of the lake's upper water column. Riverine input of 

snowmelt runoff as overflow was less of a factor in the 

development of thermal stratification because runoff 

preceded the onset of thermal stratification by about 

1 month. When thermoclines were present during 

1978-79, the epilimnion depth averaged about 12m; 

this represents about 20 percent of the lake's total 

volume on the basis of the depth-to-volume curve for 

Flathead Lake (P.P. Woods, U.S. Geological Survey, 

written commun., 2002). The upper depth limit of the 

hypolimnion during 1978-79 averaged 25 m; thus, the 

hypolimnion constituted about 58 percent of the total 

lake volume. The remaining 22 percent of lake volume 

constituted the metalimnion during thermal stratification. Similar to Coeur d'Alene Lake, Flathead Lake is 

dimictic. During 1978-79, spring circulation was in 

April, about 1 month prior to snowmelt runoff; the fall 

circulation was in early November.

Lake Pend Oreille

Lake Pend Oreille has the longest hydraulic 

residence time, 2.4 years, of the three lakes (table 5). 

That value is based on a normal full-pool volume of 

53.9 km3 divided by the mean annual outflow volume 

of 22.6 km3 . The lake's outflow volume statistics were

Physical Limnology 23
derived for a 97-year period of record (1903-2000) for 

the USGS gaging station Pend Oreille River at Newport, Washington (station 7, fig. 1) (Brennan and 

others, 2001). Annual mean outflow volume varied 

widely over that period of record, ranging from 11.5 to 

34.7 km3 . The corresponding range in hydraulic residence time was 4.7 to 1.6 years. In addition to interannual variability, outflow from the lake also varied 

widely during each year. Monthly mean outflows for 

the 1903-2000 period of record indicated that the 

mean minimum outflow volume of 1.0 km3 was in 

September, whereas the mean maximum outflow volume of 4.6 km3 was in June.

In-lake routing of the Clark Fork's inflow plume 

within Lake Pend Oreille during snowmelt runoff was 

evaluated using data and observations from several 

sources. The nutrient load/lake response study conducted during 1989-90 by the USGS and IDEQ 

included a limnological assessment of the lake's 

pelagic, or open-water, zone (Woods, 1993a). As part 

of that assessment, the vertical and horizontal distribution of the inflow plume was tracked on May 18, 1989, 

using aerial photography and in-lake profiles of specific conductance, water temperature, and percent light 

transmission (measured with an in-situ transmissometer). Inflow-plume tracking was performed a few days 

after a week of elevated Clark Fork inflow discharges, 

ranging from 1,440 to 1,850 m3/s (Harenberg and others, 1990), that were measured at the USGS gaging station Clark Fork at Whitehorse Rapids near Cabinet, 

Idaho (station 6, fig. 1). Results from the in-lake profiles showed that the more turbid river water overflowed the lake water to a depth of about 30 m. Aerial 

photographs (M.A. Beckwith, U.S. Geological Survey, 

written commun., 1989) revealed that most of the turbid riverine plume was routed into the lake's northern 

basin. However, part of the inflow plume was routed 

into the lake's southern basin, as evidenced by a decrease in transparency measured by secchi-disc readings at limnological station 2 (fig. 4); transparency 

decreased from 10 m in late April to less than 5 m during mid-May through mid-June. Runoff from snowmelt 

in 1990 began in late May and was of a longer duration 

and larger magnitude than in 1989; unfortunately, inclement weather and hazardous lake conditions prevented a repeat of the aerial photography and transmissometer profiles. However, decreased transparency 

throughout the lake's pelagic zone during June 1990 

clearly demonstrated that the turbid inflow plume was 

distributed lakewide. The shallowest transparencies

during the 1990 snowmelt runoff were in the lake's 

northern basin, indicating that the inflow plume's 

effects were more pronounced there.

The aerial photographs taken in mid-May 1989 

raised the question of why the turbid inflow plume of 

the Clark Fork was routed so distinctly into Lake Pend 

Oreille's northern basin. As shown in figure 4, the 

Clark Fork enters the lake near the approximate boundary between its northern and southern basins. Four 

physical limnological processes can be suggested as 

explanations for the plume's northward, not southward, 

destination. Two processes, wind-driven surface currents and outflow-induced currents, are unlikely because of the transitory nature of the surface currents 

and the 65-km distance from the Clark Fork inlet to the 

lake's outlet at Albeni Falls Dam. The third process, 

counterclockwise circulation induced by the Coriolis 

effect, is also unlikely because it would be expected to 

have the opposite effect: routing of the inflow plume 

southward along the lake's western margin. The fourth 

process, development of a thermal bar near the approximate boundary between the northern and southern 

basins, is the most plausible explanation. A thermal 

bar, or vertical transition zone of 4°C water separating 

littoral and pelagic water masses, results from density 

gradients produced when shallow littoral water heats 

more rapidly than pelagic water does (Wetzel, 1975). 

Although water-temperature profiles for suitably 

located positions in Lake Pend Oreille were not available with which to quantitatively evaluate this process, 

the bathymetry of the lake (fig. 4) can be used to postulate the likelihood of thermal bar development. The 

southern basin has a mean depth of 220 m, whereas the 

northern basin has a mean depth of 29 m (Woods, 

1993b), resulting in a very large difference in heat-storage capacity between these two basins. The more rapid 

warming of the northern basin could facilitate development of a thermal bar near the approximate boundary 

separating the two basins. This explanation is supported by the aerial photographs of May 18, 1989 

(shown on front cover of this report), which clearly 

show the turbid inflow plume flowing northwesterly 

along the approximate boundary between the northern 

and southern basins.

In addition to inflow-plume routing during snowmelt runoff, the limnological assessment of 1989-90 

(Woods, 1993a) produced data with which to assess the 

inflow-plume routing of the Clark Fork within Lake 

Pend Oreille during the 1989-90 non-snowmelt runoff 

periods. Frequent water-temperature measurements of

24 Fate and Transport of Nitrogen and Phosphorus, Coeur d'Alene Lake, Lake Pend Oreille, and Flathead Lake
the Clark Fork's inflow (Harenberg and others, 1990, 

1991) and numerous full-depth profiles of water temperature at limnological station 3 (fig. 4) allowed evaluation of inflow-plume routing for December through 

September of 1989 and 1990. Fifty-seven comparisons 

of river and lake temperatures indicated that overflow 

was the most common mode of inflow-plume routing, 

identified in about 75 percent of the comparisons.

Characteristics of thermal stratification and convective circulation in Lake Pend Oreille were evaluated 

(Woods, 1993a) on the basis of isopleth diagrams of 

water temperature reported for 1989-90 at limnological stations 1 through 4 (fig. 4). During 1989-90, the 

lake was thermally stratified at the three deepest (depth 

greater than 70 m) stations (1 through 3), commonly 

between June and mid-October. Thermocline depths 

ranged from 8 to 20 m in 1989 and from 8 to 16 m in 

1990. In contrast, the lake at limnological station 4 was 

shallow (depth less than 20 m) and did not thermally 

stratify for any appreciable period. The development of 

thermal stratification by early to mid-June at the two 

deepest stations in the lake's southern basin was largely 

the result of solar heating of the lake's upper water column and not the Clark Fork's input of snowmelt runoff, 

which was routed as overflow, primarily through the 

lake's shallow northern basin, during May and June. 

Water-column turbulence generated by such inflowplume routing likely inhibited the development of thermal stratification at limnological station 4, owing to 

shallow depth. In contrast, the lake at limnological station 3 in the northern basin was thermally stratified, 

through a combination of inflow-plume routing as 

overflow and solar heating of the lake's upper water 

column. During 1989-90 and when thermoclines were 

present, the epilimnion depth averaged about 15m; this 

represents about 7 percent of the lake's total volume, 

on the basis of the depth-to-volume curve for Lake 

Pend Oreille developed by Fields and others (1996). 

The upper depth limit of the hypolimnion over the 

same period averaged 30 m; thus, the hypolimnion constituted about 85 percent of the total lake volume. The 

remaining 8 percent of lake volume constituted the 

metalimnion. Similar to the other lakes, Lake Pend 

Oreille is dimictic; however, such circulation may not 

extend full depth during each occurrence. Spring circulation during 1989-90 was in April; the fall circulation 

was in mid-October of both years.

CHEMICAL AND BIOLOGICAL LIMNOLOGY

Overview

Hydrologic and constituent budgets, in conjunction with drainage basin and physical limnological 

characteristics, are important tools for evaluating fate 

and transport of constituents within a lake. However, 

the quantitative differences between input and output 

loads represent the net influence of limnological processes because constituent loads output from a lake 

result from the integration of all hydrologic, physical, 

chemical, and biological processes that operate within 

the lake. To distinguish the hydrologic and physical 

limnological effects on constituent fate and transport 

from those associated with chemical and biological 

processes, the third phase in the evaluation, discussed 

in this section, focuses on spatial and temporal variations in chemical and biological characteristics within 

each lake's water mass.

Subsequent to their delivery into a lake as dissolved, colloidal, and particulate fractions, nonconservative nutrients such as nitrogen and phosphorus can 

be involved in a variety of chemical and biological processes. Both nitrogen and phosphorus are involved in 

biological processes because they are essential for phytoplankton production. Phytoplankton assimilation of 

dissolved inorganic nitrogen (nitrite, nitrate, and 

ammonia) and orthophosphorus converts some of the 

dissolved fraction to a particulate, organically bound 

fraction that has several possible fates. Advective transport physically redistributes the particles within the 

lake, a part of which may exit the lake as an outflow 

load. The particles also can be retained within the 

water column by turbulence and be subjected to remineralization or uptake by zooplankton grazing. Dissolved and colloidally bound fractions are subject to inlake sedimentation when converted to particles by processes such as assimilation, precipitation, complexation, and adsorption. Sedimentation delivers the particles to the lakebed, where they may be subjected to 

remineralization and possible recycling back into the 

water column; alternatively, subsequent sedimentation 

may permanently bury the particles within the lakebed.

Many of these chemical and biological processes 

are dynamic and transient; they occur over short timeframes (seconds to days) and, thus, are difficult to 

quantify and evaluate accurately when limnological 

samples are collected over weekly or longer timeChemical and Biological Limnology 25
frames. Limnological sampling at these three lakes was 

conducted over timeframes of 2 to 8 weeks. Consequently, much of the following evaluation of chemical 

and biological limnology focuses on spatial and temporal comparisons of mean conditions among the three 

lakes.

Trophic State

One of the primary reasons that nutrient loading 

has been assessed for many lakes was to evaluate biological productivity in relation to nutrient enrichment, 

or eutrophication; such is the case for Coeur d'Alene 

and Flathead Lakes and Lake Pend Oreille. Trophic 

state provides the initial comparison of chemical and 

biological limnology among the three lakes.

Trophic state refers to the biological productivity 

of a water body and integrates the physical, chemical, 

and biological processes within that water body. For 

ease of categorization, three trophic states commonly 

are defined: oligotrophic (low productivity), mesotrophic (intermediate productivity), and eutrophic (high 

productivity). Numerous variables have been employed 

as a basis for trophic-state classification. Although no 

classification system is universally accepted, variables 

such as total phosphorus, total nitrogen, chlorophyll-a,

and secchi-disc transparency frequently have been used 

to classify trophic state. The United Nation's Organization for Economic Cooperation and Development used 

these four variables to develop a statistically based, 

open-boundary, trophic-state classification system 

(Ryding and Rast, 1989), which is shown in table 6. An 

open-boundary system compensates for the overlap in 

classification that commonly occurs with fixed-boundary, or single-value, systems. Under the open-boundary 

system, a water body is considered to be classified correctly if three of the four upper water-column variables 

are within two standard deviations of their geometric 

mean for the same trophic state.

On the basis of annual geometric mean values for 

upper water-column concentrations of total phosphorus, 

total nitrogen, chlorophyll-0, and transparency (table 7), 

all three lakes can be classified as oligotrophic. Even 

though the three lakes received very different quantities 

of nitrogen and phosphorus from their drainage basins 

(tables 1-3), their biological responses, expressed as 

trophic state, were quite similar.

Another important water-quality characteristic 

used to delineate trophic state is hypolimnetic dissolved oxygen. As lake productivity increases, 

decreases in hypolimnetic dissolved oxygen often 

result when biological and chemical oxygen demands

Table 6. Trophic-state classification based on open-boundary values for four 

limnological variables

, micrograms per liter; m, meters; x, annual geometric mean; SD, standard deviation]

Variable, unit 1

Total phosphorus (ng/L)

Total nitrogen (ng/L)

Chlorophyll-a (ugfl,)

Secchi-disc transparency (m)

X

x±lSD 

x ± 2SD

X

*±1SD 

x ± 2SD

x 

*±1SD 

*±2SD

x 

*±1SD 

x ± 2SD

Oligotrophic

8.0 

4.8-13.3 

2.9-22.1

661

371-1,180 

208-2,103

1.7 

.8-3.4 

.4-7.1

9.9 

5.9-16.5

3.6-27.5

Mesotrophic

26.7 

14.5-49.0 

7.9-90.8

753 

485-1,170 

313-1,816

4.7 

3.0-7.4 

1.9-11.6

4.2 

2.4-7.4 

1.4-13.0

Eutrophic

84.4 

48.0-189 

16.8-424

1,875 

861-4,081 

395-8,913

14.3 

6.7-31.0 

3.1-66.0

2.4 

1.5-4.0 

.9-6.7

1 Modified from Ryding and Rast (1989).

26 Fate and Transport of Nitrogen and Phosphorus, Coeur d'Alene Lake, Lake Pend Oreille, and Flathead Lake
Table 7. Trophic state of Coeur d'Alene Lake and Lake Pend Orei.lle, 

Idaho, and Flathead Lake, Montana, based on annual mean values 

for four limnological variables

, micrograms per liter; m, meters; TS, trophic state; O, oligotrophic; 

M, mesotrophic]

Year

Total

phosphorus 

(H9/I-)

X 1 TS

Total

nitrogen 

(H9/L)

X 1 TS

Chlorophyll-a 

(H9/L)

X 1 TS

Secchi-disc

transparency 

(m)

X 2 TS

Coeur d'Alene :

1991

1992

5.6

4.6

O

O

282

206

O

O

0.43

.79

O

O

4.0

2.9

M

M

Flathead'

1978-82 7.4 O 120 O 1.2 O 8.8 | O

Pend Oreille -

1989

1990

9.0

6.5

O

O

142

116

O

O

.8

.8

O

O

7.0

6.3

O

O

1 Lakewide, annual geometric mean concentration within upper water 

column for Coeur d'Alene Lake and Lake Pend Oreille. Annual mean concentration at mid-lake station for Flathead Lake.

2 Lakewide, annual geometric mean for Coeur d'Alene Lake and Lake 

Pend Oreille. Annual mean at mid-lake station for Flathead Lake.

3 Data from Woods and Beckwith (1997).

4 Data from Stanford and others (1983) and Stuart (1983).

5 Data from Woods (1993a).

exceed the oxygen mass within the hypolimnion. The 

oligotrophic nature of these three lakes (table 7) indicates a small potential for development of a hypolimnetic dissolved oxygen deficit. On the basis of watercolumn profiles of dissolved oxygen concentrations for 

Coeur d'Alene Lake (Woods and Beckwith, 1997), 

Flathead Lake (Stuart, 1983), and Lake Pend Oreille 

(Woods, 1993a), the three lakes have well-oxygenated 

hypolimnia.

Hypolimnetic Nutrient Storage

Most biological production in lakes is within the 

well-mixed upper water column (epilimnion), where 

solar radiation is sufficient to drive phytoplankton photosynthesis. A notable difference among these three 

lakes is the percentage of epilimnion volume in relation 

to total lake volume: Lake Pend Oreille is 7 percent 

epilimnion, Flathead Lake is 20 percent epilimnion, 

and Coeur d'Alene Lake is 38 percent epilimnion. Relative to the total volume, Lake Pend Oreille has the 

smallest epilimnetic volume in which to convert nutrients into phytoplankton biomass. Conversely, and in 

relation to total volume, Lake Pend Oreille has the largest hypolimnetic volume; Coeur d'Alene Lake has the 

smallest. In contrast to phytoplankton photosynthesis, 

remineralization throughout the water column converts 

particulate constituents into dissolved constituents 

throughout the year; however, the hypolimnion is the 

primary strata for remineralization. During thermal 

stratification, which often coincides with the period of 

elevated biological production, the hypolimnion receives the downward "rain" of organic and inorganic 

constituents delivered into the lake or produced in the 

epilimnion and metalimnion. If convective circulation 

is strong enough to mix the entire water column, hypolimnetic water can serve as a source of remineralized 

nutrients to augment biological production within the 

epilimnion. As lake depth increases, the potential for 

convective circulation to mix the entire water column 

decreases. The increase in depth also implies longer 

residence times for nutrient remineralization and a 

larger hypolimnetic volume for nutrient storage. In a 

large, deep lake such as Lake Pend Oreille, convective 

circulation of hypolimnetic nutrients into the epilimnion may occur only sporadically. In contrast, in a shallower lake such as Coeur d'Alene Lake, convective circulation of hypolimnetic nutrients into the epilimnion 

may occur twice a year. Compared with Lake Pend 

Oreille and Coeur d'Alene Lake, Flathead Lake represents an intermediate example because of its moderate 

depth and substantial exposure to wind.

A comparison of hypolimnetic enrichment of total 

nitrogen among the three lakes indicates that annual 

mean concentrations of total nitrogen were larger in the 

hypolimnia than in the epilimnia (table 8). The ratios of 

epilimnetic to hypolimnetic concentrations ranged 

from 0.67 (Lake Pend Oreille in 1990) to 0.79 (Coeur 

d'Alene Lake in 1992). The relative difference between 

epilimnetic to hypolimnetic nitrogen concentrations 

was smallest in Coeur d'Alene Lake, the shallowest 

and most likely to undergo full-depth convective 

circulation. One possible explanation for that lake's 

enriched hypolimnetic total nitrogen can be derived 

from the results of a 1999 study of benthic flux in 

Coeur d'Alene Lake done by the USGS (Kuwabara and 

others, 2000). Using an in-situ benthic flux chamber, 

the annual flux of dissolved inorganic nitrogen, a component of total nitrogen, from the lakebed sediments to

Chemical and Biological Limnology 27
Table 8. Annual mean concentrations of total nitrogen and 

phosphorus within the epilimnion and hypolimnion at the deepest 

limnological stations, Coeur d'Alene Lake and Lake Pend Oreille, 

Idaho, and Flathead Lake, Montana

[|j,g/L, micrograms per liter; EPI, epilimnion; HYPO, hypolimnion]

Year

Total nitrogen

(ng/L)

EPI 1 HYPO2

EPI

HYPO

Total phosphorus 

(H9/L)

EPI 1 HYPO2

EPI

HYPO

Coeur d'Alene •*

1991

1992

292

216

375

274

0.78

.79

4.6

2.9

4.8

2.8

0.96

1.04

Flathead 4

Sept. 1991- 

Aug. 1993 128 182 .70 5.1 5.8 .88

Pend Oreille 5

1989

1990

160

110

212

164

.75

.67

8

6

10

10

.80

.60

1 When water column not thermally stratified, refers to upper water 

column.

2 When water column not thermally stratified, refers to lower water 

column.

3 Limnological station 3 (fig. 2), data from Woods and Beckwith 

(1997).

4 Limnological station 2 (fig. 3), data from Stanford and others (1994).

5 Limnological station 2 (fig. 4), data from Woods (1993a).

the overlying water column was calculated to be 270 

jag/cm2 . On the basis of that result and riverine loading 

data from Woods (2001), the contribution of nitrogen to 

Coeur d'Alene Lake from benthic flux was determined 

to exceed that delivered to the lake from its drainage 

basin by a factor of 1.5. Comparable studies of benthic 

flux have not been done for Flathead Lake or Lake 

Pend Oreille. Relative differences between epilimnetic 

and hypolimnetic total nitrogen concentrations were 

similar for those two lakes, regardless of large differences in their depth.

On the basis of epilimnetic to hypolimnetic ratios 

of phosphorus concentration, which ranged from 0.60 

(Lake Pend Oreille in 1990) to 1.04 (Coeur d'Alene 

Lake in 1992), the three lakes represent a gradient in 

hypolimnetic enrichment of total phosphorus (table 8). 

Lake Pend Oreille exhibited a clearly defined case of 

hypolimnetic enrichment, presumably because of its 

large depth. Coeur d'Alene Lake exhibited the opposite 

condition, no enrichment of hypolimnetic total phosphorus, presumably because of its shallow depth and 

short hydraulic residence time.

Nutrient Partitioning

Additional insight into chemical and biological 

limnology can be gained through analysis of the partitioning of nutrients into their bioavailable and particulate fractions. The bioavailable fractions of nitrogen 

and phosphorus are defined here, respectively, as the 

sum of dissolved (<0.45 jam) nitrite, nitrate, and ammonia and dissolved orthophosphorus. The following two 

comparisons were made: (1) epilimnion and hypolimnion, and (2) inflow loads and outflow loads.

EPILIMNION AND HYPOLIMNION

In 1991, the mean percentages of bioavailable 

nitrogen and particulate nitrogen in the hypolimnion of 

Coeur d'Alene Lake were 25 and 75, respectively; 

whereas in the epilimnion, the mean percentages were 

14 and 86, respectively (fig. 5). The percentage compositions between the epilimnion and hypolimnion were 

even more dissimilar in 1992. The percentages of bioavailable and particulate nitrogen between the epilimnion and hypolimnion in Flathead Lake were comparable; in both strata, bioavailable nitrogen composed 

about 30 percent of total nitrogen. As in Coeur d'Alene 

Lake, percentages of bioavailable and particulate nitrogen between the epilimnion and hypolimnion of Lake 

Pend Oreille also were dissimilar. However, in contrast 

to the other two lakes, bioavailable nitrogen in Lake 

Pend Oreille's hypolimnion composed between 61 and 

73 percent of total nitrogen, indicative of extensive 

remineralization and retention.

Among the three lakes, the overall pattern for bioavailable and particulate phosphorus composition, in 

relation to total phosphorus, was similar to that for 

nitrogen (fig. 5). The percentage difference between 

epilimnetic and hypolimnetic bioavailable phosphorus 

in Coeur d'Alene Lake was less than 10 percent in 

1991 and 1992. Bioavailable phosphorus in both the 

epilimnion and hypolimnion composed a larger percentage of total phosphorus in 1992 than in 1991 but 

was still less than 50 percent. In Flathead Lake, bioavailable phosphorus in the epilimnion and hypolimnion composed only 14 and 12 percent of total phosphorus, respectively. In contrast, the percentage composition of phosphorus in the epilimnion and hypolim28 Fate and Transport of Nitrogen and Phosphorus, Coeur d'Alene Lake, Lake Pend Oreille, and Flathead Lake
Nitrogen1

IUU

90

80

70 

60 

50

O

fc 30

5 20

O

U 10

W

O

I

-

-

-

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COEUR D'ALENE LAKE3

1991-93 

FLATHEAD LAKE4

EXPLANATION

" .A.V ^V .rco 

\{y *V^ W*

1989 1990 

LAKE PEND OREILLE5

3 Limnological station 3 (fig. 2), data from Woods and 

Beckwith (1997)

I__I Bioavailable

I__I Particulate

4 Limnological station 2 (fig. 3), data from Stanford and

i Bioavailable nitrogen defined as sum of dissolved nitrite, nitrate, and others (1994) 

ammonia; particulate nitrogen defined as total minus bioavailable

2 Bioavailable phosphorus defined as dissolved orthophosphorus; 

particulate phosphorus defined as total minus bioavailable

5 Limnological station 2 (fig. 4), data from Woods (1993a)

Figure 5. Annual mean percentage composition of bioavailable and particulate nitrogen and phosphorus concentrations, in relation to total 

nitrogen and phosphorus concentrations, respectively, within the epilimnion and hypolimnion at the deepest limnological stations, Coeur 

d'Alene Lake and Lake Pend Oreille, Idaho, and Flathead Lake, Montana.

Chemical and Biological Limnology 29
nion of the deepest of the three lakes, Pend Oreille, was 

substantially different. Within the epilimnion, bioavailable phosphorus composed 35 percent, on average, of 

total phosphorus; that percentage increased to 75 

within the hypolimnion. As with nitrogen, this increase 

was indicative of significant remineralization and 

retention of phosphorus within the hypolimnion of 

Lake Pend Oreille.

INFLOW LOADS AND OUTFLOW LOADS

The annual mean percentage composition of bioavailable and particulate nitrogen and phosphorus, in 

relation to total concentrations of nitrogen and phosphorus in inflow and outflow loads for the three lakes, 

are listed in figure 6. The information in figure 6 was 

combined with that in tables 1-3 to produce figures 

7-11, which were used to help separate physical limnological processes from those of a chemical and (or) 

biological nature.

Inflow and outflow loads of bioavailable and particulate nitrogen for Coeur d'Alene Lake showed little 

difference in their percentage composition with respect 

to total nitrogen; the percentages were comparable 

between 1991 and 1992 (figs. 7 and 8). Such results 

might indicate that the lake merely passed its inflow 

nitrogen load through to its outlet relatively unaltered; 

the lake retained less than 10 percent of the nitrogen it 

received as input in both years. However, other data 

suggest chemical and biological alteration of the lake's 

inflow load of nitrogen. Phytoplankton assimilation of 

bioavailable nitrogen was evident from changes in dissolved inorganic nitrogen concentrations periodically 

measured at limnological stations I through 6 (fig. 2) 

during 1991-92. Within the lake's upper water column, dissolved inorganic nitrogen concentrations 

ranged from less than 7 to 234 ^ig/L during 1991 and 

from less than 7 to 98 ^ig/L during 1992 (Harenberg 

and others, 1992, 1993). During both years, the minimum concentrations were measured during May 

through September, the period of thermal stratification 

and summer phytoplankton production. The aforementioned addition of dissolved inorganic nitrogen from 

benthic flux from the lakebed sediments provided an 

internal source of bioavailable nitrogen that replaced 

part of the influent bioavailable nitrogen that was converted to particulate nitrogen within the lake.

Similar to nitrogen loads, the inflow and outflow 

loads of bioavailable and particulate phosphorus for 

Coeur d'Alene Lake showed little difference in their

percentage composition with respect to total phosphorus (figs. 7 and 8). However, unlike its retention of 

nitrogen, the lake's retention of phosphorus was about 

two-thirds of its input in 1991 and about one-third in 

1992. If physical settling were the only limnological 

process affecting influent phosphorus loads, then the 

percentage of bioavailable phosphorus would have 

increased at the lake's outlet; however, such was not the 

case. Chemical and biological processes within the lake 

also affected the influent phosphorus loads. The propensity to sorb to particulate matter probably converted 

part of the bioavailable phosphorus to particulate phosphorus. Phytoplankton assimilation also converted bioavailable phosphorus into particulate phosphorus. Dissolved orthophosphorus concentrations within the 

upper water column of limnological stations 1 through 

6 (fig. 2) ranged from less than 1 to 11 jag/L in 1991 

and from less than 1 to 6 |^g/L in 1992 (Harenberg and 

others, 1992, 1993). The minimum concentrations of 

dissolved orthophosphorus were measured during the 

summer months of both years, indicative of phytoplankton assimilation.

In contrast to Coeur d'Alene Lake, Flathead Lake 

retained about 36 percent of its influent nitrogen load 

from drainage basin and atmospheric sources during 

1978-82 (fig. 9). The percentage of bioavailable nitrogen, in relation to total nitrogen, for Flathead Lake's 

drainage basin input was 42; that declined to 23 at the 

lake's outlet (fig. 9), indicative of in-lake conversion of 

bioavailable nitrogen to particulate nitrogen by chemical and biological processes. These results are consistent with seasonal dynamics of dissolved nitrite plus 

nitrate concentrations at Flathead Lake's deepest limnological station, 2 (fig. 3), as presented by Stanford 

and others (1997) for water years 1990-96. Within the 

upper water column, concentrations ranged from less 

than 1 to 63 |^g/L; the smallest concentrations were 

measured during the summer months of elevated phytoplankton production.

Flathead Lake retained about three-fourths of the 

phosphorus it received from drainage basin and atmospheric sources (fig. 9). The percentage composition of 

inflow and outflow loads of bioavailable phosphorus in 

relation to total phosphorus were nearly equal—both 

were less than 10 percent. As mentioned previously, if 

physical settling were the only limnological process 

affecting influent phosphorus loads, then the percentage of bioavailable phosphorus would have increased 

between the lake's inlet and outlet. Given the likelihood 

of a substantial removal of sediment-associated phos30 Fate and Transport of Nitrogen and Phosphorus, Coeur d'Alene Lake, Lake Pend Oreille, and Flathead Lake
Nitrogen1

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COEUR D'ALENE LAKE3

1991-93 

FLATHEAD LAKE4

1989 1990 

LAKE PEND OREILLE5

3 Inflow concentrations from Coeur d'Alene and St. Joe 

Rivers; outflow concentrations from Spokane River

EXPLANATION

[_I Bioavailable

I I Particulate

4 Inflow and outflow concentrations from Flathead River

1 Bioavailable nitrogen defined as sum of dissolved nitrite, nitrate, and

ammonia; particulate nitrogen defined as total minus bioavailable 5 Inflow concentrations from Clark Fork; outflow concentrations from Pend Oreille River

2 Bioavailable phosphorus defined as dissolved orthophosphorus; 

particulate phosphorus defined as total minus bioavailable

Figure 6. Annual mean percentage composition of bioavailable and particulate nitrogen and phosphorus concentrations, in relation to total 

nitrogen and phosphorus concentrations, respectively, for inflows and outflows, Coeur d'Alene Lake and Lake Pend Oreille, Idaho, and 

Flathead Lake, Montana.

Chemical and Biological Limnology 31
TOTAL NITROGEN

Watershed input

2,080,000 kilograms 

82% paniculate 

18% bioavailable

Atmospheric input

75,000 kilograms

11111

Coeur d'Alene Lake 

(Watershed + Atmospheric inputs - Lake output):

125,000 kilograms

Lake output

2,030,000 kilograms 

81% particulate 

19% bioavailable

TOTAL PHOSPHORUS

Watershed input

108,000 kilograms 

74% particulate 

26% bioavailable

Atmospheric input

6,500 kilograms

11111

Coeur d'Alene Lake 

(Watershed + Atmospheric inputs - Lake output)=

78,400 kilograms

Lake output

36,100 kilograms 

71% particulate 

29% bioavailable

Figure 7. Relation between inputs and outputs of total nitrogen and phosphorus and nutrient partitioning of input and output 

loads, Coeur d'Alene Lake, Idaho, 1991 calendar year.

32 Fate and Transport of Nitrogen and Phosphorus, Coeur d'Alene Lake, Lake Pend Oreille, and Flathead Lake
TOTAL NITROGEN

Watershed input

870,000 kilograms 

80% paniculate 

20% bioavailable

Atmospheric input

75,000 kilograms

Y t I T Y

Coeur d'Alene Lake 

(Watershed + Atmospheric inputs — Lake output)=

85,000 kilograms

Lake output

860,000 kilograms 

76% participate 

24% bioavailable

TOTAL PHOSPHORUS

Watershed input

37,100 kilograms 

61% paniculate 

39% bioavailable

Atmospheric input

6,500 kilograms

I I I I T

Coeur d'Alene Lake 

(Watershed + Atmospheric inputs - Lake output)=

16,000 kilograms

Lake output

27.600 kilograms 

65% paniculate 

35% bioavailable

Figure 8. Relation between inputs and outputs of total nitrogen and phosphorus and nutrient partitioning of input and output 

loads, Coeur d'Alene Lake, Idaho, 1992 calendar year.

Chemical and Biological Limnology 33
TOTAL NITROGEN

Atmospheric input

175,000 kilograms

I I 1 I I

Watershed input

1,420,000 kilograms 

58% particulate 

42% bioavailable

Flathead Lake 

(Watershed + Atmospheric inputs - Lake output):

570,000 kilograms

Lake output

1,020,000 kilograms 

77% particulate 

23% bioavailable

TOTAL PHOSPHORUS

Atmospheric input

29,000 kilograms

Watershed input

213,000 kilograms 

94% particulate 

6% bioavailable

Flathead Lake 

(Watershed + Atmospheric inputs — Lake output):

183,000 kilograms

Lake output

59,000 kilograms 

92% particulate 

8% bioavailable

Figure 9. Relation between inputs and outputs of total nitrogen and phosphorus and nutrient partitioning of input and output 

loads, Flathead Lake, Montana, 1978-82.

34 Fate and Transport of Nitrogen and Phosphorus, Coeur d'Alene Lake, Lake Pend Oreille, and Flathead Lake
TOTAL NITROGEN

Watershed input

4,220,000 kilograms 

61% particulate 

39% bioavailable

Atmospheric input

190,000 kilograms

11111

Lake Pend Oreille 

(Watershed + Atmospheric inputs - Lake output)=

670,000 kilograms

Lake output

3,740.000 kilograms 

72% particulate 

28% bioavailable

TOTAL PHOSPHORUS

Atmospheric input

19,000 kilograms

I I I T I

Watershed input

307,000 kilograms 

70% particulate 

30% bioavailable

Lake Pend Oreille 

(Watershed + Atmospheric inputs - Lake output)=

55,000 kilograms

Lake output

271,000 kilograms 

85% particulate 

15% bioavailable

Figure 10. Relation between inputs and outputs of total nitrogen and phosphorus and nutrient partitioning of input and output 

loads, Lake Pend Oreille, Idaho, 1989 water year.

Chemical and Biological Limnology 35
TOTAL NITROGEN

Watershed input

5,480,000 kilograms 

68% paniculate 

32% bioavailable

Atmospheric input

190,000 kilograms

1 1 I I I

Lake Pend Oreille 

(Watershed + Atmospheric inputs - Lake output):

840,000 kilograms

Lake output

4,830,000 kilograms 

80% paniculate 

20% bioavailable

TOTAL PHOSPHORUS

Watershed input

389,000 kilograms 

76% paniculate 

24% bioavailable

Atmospheric input

19,000 kilograms

I I 1 1 1

Lake Pend Oreille 

(Watershed + Atmospheric inputs - Lake output):

55,000 kilograms

Lake output

353,000 kilograms 

84% paniculate 

16% bioavailable

Figure 11. Relation between inputs and outputs of total nitrogen and phosphorus and nutrient partitioning of input and output 

loads, Lake Pend Oreille, Idaho, 1990 water year.

36 Fate and Transport of Nitrogen and Phosphorus, Coeur d'Alene Lake, Lake Pend Oreille, and Flathead Lake
phorus by physical settling, the large percentage composition of participate phosphorus output from the lake 

indicates conversion of bioavailable phosphorus into 

particulate phosphorus by adsorption and phytoplankton assimilation. These results are consistent with the 

seasonal dynamics of bioavailable phosphorus concentrations at Flathead Lake's lirnnological station 2 (fig. 

3) during water years 1990-96 (Stanford and others, 

1997). Within the upper water column, bioavailable 

phosphorus concentrations ranged from 0.4 to 

4.1 p,g/L; the smallest concentrations were measured 

during the summer months of elevated phytoplankton 

production.

During water years 1989 and 1990, Lake Pend 

Oreille retained about 15 percent of the nitrogen load it 

received from drainage basin and atmospheric inputs 

(figs. 10 and 11). Phytoplankton assimilation of bioavailable nitrogen was indicated by the reduction in the 

percentage of bioavailable nitrogen at the lake outlet 

compared with that from drainage basin inflow 

(between 11 and 12 percent) (figs. 10 and 11). Again, 

these results are consistent with upper water-column 

concentrations of dissolved inorganic nitrogen at lirnnological stations 2 and 3 (fig. 4), which ranged from 

10 to 144 p,g/L over the 2-year period (Harenberg and 

others, 1991, 1992); the smallest concentrations were 

measured during the summer months of elevated phytoplankton production.

Of the three lakes, Lake Pend Oreille retained the 

smallest percentage of its input total phosphorus load; 

about 17 in 1989 and 13.5 in 1990 (figs. 10 and 11). In 

both years, the percentage of bioavailable phosphorus, 

in relation to total phosphorus, input to the lake was 

reduced at the lake outlet by 15 percent in 1989 and 

by 8 percent in 1990 (figs. 10 and 11). As in the other 

two lakes, that shift in percentage composition indicated conversion of bioavailable phosphorus to particulate phosphorus by processes such as adsorption and 

phytoplankton assimilation. Upper water-column concentrations of dissolved orthophosphorus at lirnnological stations 2 and 3 (fig. 4) ranged from less than 1 to 7 

p,g/L over the 2-year period (Harenberg and others, 

1991, 1992). As with dissolved inorganic nitrogen, the 

smallest concentrations of dissolved orthophosphorus 

were measured during the summer months.

FATE AND TRANSPORT OF NUTRIENT 

LOADS

Overview

Coeur d'Alene and Rathead Lakes and Lake Pend 

Oreille received, discharged, and retained a wide range 

of nitrogen and phosphorus loads, in an absolute and 

relative sense (tables 1-3). The three lakes also displayed a wide range of physical lirnnological characteristics (table 5); selected values from those four tables 

are summarized in table 9. If only morphometric and 

empirically derived values such as mean and maximum 

depth, hydraulic residence time, and trap efficiency 

were considered, the lake with the largest values, Lake 

Pend Oreille, would be expected to retain the largest 

percentage of the total nitrogen and phosphorus load 

received. However, that was not the case—Flathead 

Lake retained the largest loads of total nitrogen and 

phosphorus relative to what it received. Coeur d'Alene 

Lake, with the smallest values for mean and maximum

Table 9. Summary of retained load/input load for total 

nitrogen and phosphorus and selected physical lirnnological 

characteristics, Coeur d'Alene Lake and Lake Pend Oreille, 

Idaho, and Flathead Lake, Montana

[m, meters; cy, calendar year; wy, water year; yr, year]

Variable, 

unit

Coeur d'Alene '• 2

1991 cy 1992 cy

Flathead L 2

1978-82

Pend Oreille '• 2

1989 

wy

1990 

wy

Retained load Vinput load, percent

Total nitrogen

Total 

phosphorus

Mean depth, 

m

Maximum 

depth, m

Hydraulic 

residence 

time, yr

Trap 

efficiency, 

percent

6

69

9

37

21.7

63.7

.50

93

36

4 76

50.2

113

2.2

97

15 15

17 14

164

357

2.4

98

1 Data from tables 1-3.

2 Data from table 5.

3 Input load - output load.

Fate and Transport of Nutrient Loads 37
depth, hydraulic residence time, and trap efficiency, 

retained a larger relative load of total phosphorus than 

did Lake Pend Oreille; Coeur d'Alene Lake's retention 

of total nitrogen was slightly smaller than that of Lake 

Pend Oreille.

The unexpected behavior of Lake Pend Oreille 

suggests that limnological processes other than simple 

physical sedimentation affected the fate and transport 

of nutrient loads delivered to that lake. Likewise, the 

large sedimentary loss of particulate phosphorus within 

Flathead Lake is not intuitively obvious if only the lack 

of change in nutrient partitioning between the lake's 

inlet and outlet is considered. For each of these lakes, 

the influence of in-lake chemical and biological processes was evident, on the basis of shifts in nutrient 

partitioning between the dissolved and particulate fractions for input and output loads. However, a rigorous 

evaluation of chemical and biological processes was 

not possible because of the need to focus on mean conditions; sampling intervals were too long to adequately 

quantify and evaluate the temporal nature of those processes. Regardless, by coordinating the evaluation of 

shifts in nutrient partitioning with the evaluation of 

load discharged versus load received, insight can be 

gained into the importance of interactions among physical, chemical, and biological processes that affect the 

fate and transport of nutrient loads delivered into the 

three lakes.

Coeur d'Alene Lake

Among the three lakes, Coeur d'Alene Lake had 

the smallest input and output loads of total nitrogen and 

phosphorus. Compared with the other two lakes, it also 

had the shortest hydraulic residence time, shallowest 

mean and maximum depths, and narrowest shape. 

Because these physical factors are associated with an 

increased potential for turbulent, advective transport of 

dissolved, colloidal, and particulate constituents, Coeur 

d'Alene Lake would be expected to retain a smaller 

proportion of its input loads, compared with those of 

the other two lakes.

Indeed, Coeur d'Alene Lake retained less than 

9 percent of the total nitrogen it received (table 9). An 

important factor in the lake's small retention of its input 

load of total nitrogen was the temporal distribution of 

input loads. On the basis of graphical plots of daily 

loads delivered into Coeur d'Alene Lake over the 1999

water year, Woods (2001) reported that about 

56 percent of the annual load of total nitrogen was 

delivered during April through June, the period of 

snowmelt runoff during which advective transport 

through the lake as overflow is most likely. The narrowness of the lake's main channel (fig. 2) and the 

location of the two primary tributaries near the lake's 

southern end are likely to enhance advective transport, 

compared with transport expected in a more circular 

lake basin. Physical sedimentation of total nitrogen 

does occur; the mean concentration of total nitrogen 

in lakebed sediments from 20 sampling locations 

throughout Coeur d'Alene Lake was 2,100 mg/kg 

(Woods and Beckwith, 1997). Even in the absence of 

large shifts in partitioning between bioavailable and 

particulate nitrogen for input and output loads (fig. 6), 

the biological process of phytoplankton assimilation 

was indicated by decreases in upper water-column concentrations of dissolved inorganic nitrogen.

Chemical processes, in the form of hypolimnetic 

remineralization of particulate to bioavailable nitrogen 

and the addition of dissolved inorganic nitrogen from 

the lakebed sediments by benthic flux, also affected 

total nitrogen concentrations and partitioning in the 

lake. The effect of hypolimnetic enrichment of bioavailable nitrogen by remineralization and benthic flux 

was evaluated for the 1999 water year as part of a joint 

EPA/USGS assessment of trace-element and nutrient 

loading for Coeur d'Alene Lake (URS Greiner Inc., 

and CH2M-Hill Inc., 200Ib). Input loads substantially 

exceeded output loads of bioavailable nitrogen during 

December and January but were about equal during 

May through November. During February through 

April, the lake discharged substantially more bioavailable nitrogen than it received. The net loss of bioavailable nitrogen during those 3 months was a consequence 

of full-depth convective mixing, which was associated 

with advective transport and discharge of part of the 

bioavailable nitrogen produced in the hypolimnion by 

remineralization and benthic flux.

The propensity for phosphorus to sorb to inorganic and organic particles suggests that Coeur d'Alene 

Lake would retain a larger proportion of its input load 

for phosphorus than for nitrogen. Such was the case; 

the lake retained between one-third and two-thirds of 

its annual input load of total phosphorus (table 9). 

About 80 percent of that annual input was delivered 

during April through June, on the basis of graphical 

plots of daily loads delivered into Coeur d'Alene Lake 

over the 1999 water year (Woods, 2001). The results of

38 Fate and Transport of Nitrogen and Phosphorus, Coeur d'Alene Lake, Lake Pend Oreille, and Flathead Lake
lakebed sediment analyses in Coeur d'Alene Lake 

clearly indicate that sedimentation of total phosphorus 

occurs; the mean concentration of total phosphorus in 

lakebed sediments was 940 mg/kg (Woods and Beckwith, 1997). Nonetheless, sedimentation and advective 

transport were not the only limnological processes in 

Coeur d'Alene Lake that affected phosphorus loads 

delivered to the lake. Part of the bioavailable phosphorus was converted into particulate phosphorus by the 

chemical process of adsorption and the biological process of phytoplankton assimilation, as indicated by 

minimal shifts in partitioning between inflow and outflow loads (fig. 6), despite the reduction in total load 

magnitude.

The adsorption of bioavailable phosphorus in the 

lake was postulated as an important chemical process 

because the lakebed sediments are rich in iron oxides 

and hydroxides, for which bioavailable phosphorus has 

a high adsorption affinity (Wetzel, 1975; Elder, 1988). 

The mean concentration of total iron measured in about 

150 surficial lakebed samples from Coeur d'Alene 

Lake was 51,000 mg/kg (Horowitz and others, 1993). 

Only 14 percent of 1,317 analyses of soils in the conterminous United States (Shacklette and Boerngen, 

1984) contained iron concentrations in excess of those 

measured in the lakebed of Coeur d'Alene Lake. The 

lake receives abundant amounts of iron in the inflow 

from the Coeur d'Alene River. According to Hem 

(1985), flowing, well-aerated, nonacidic surface water 

generally contains less than 10 p,g/L dissolved iron. 

During the 2001 water year, however, dissolved iron 

concentrations in the Coeur d'Alene River ranged from 

20 to 190 fig/L (O'Dell and others, 2002). The lake's 

retention of one-third to two-thirds of its influent phosphorus load, in spite of its short hydraulic residence 

time and shallow depths, may have been increased by 

its potential to form particulate phosphorus within the 

water column.

Flathead Lake

Both input and output loads of total nitrogen and 

phosphorus for Flathead Lake were intermediate between those of the other two lakes. Flathead Lake's 

hydraulic residence time and trap efficiency were comparable to those of Lake Pend Oreille, whereas mean 

and maximum depths were about twice those of Coeur 

d'Alene Lake and only about one-third those of Lake 

Pend Oreille. Of the three lakes, Flathead had the longest dimensions for length and width, both maximum 

and effective, and had the largest surface area. Because 

of its empirically determined ability to retain dissolved, 

colloidal, and particulate constituents, Flathead Lake 

would be expected to retain a large proportion of its 

input loads.

Consistent with this expectation, Flathead Lake 

retained the largest proportion of its input load of total 

nitrogen, 36 percent (table 9). About 60 percent of that 

input load was delivered to the lake during April 

through June, the period of snowmelt runoff (Stanford 

and others, 1997). Although the lake's inflow plume 

has been routed in a rather complex fashion in some 

years, in other years, the plume has been routed more 

directly to the lake's southern outlet (Stuart, 1983). The 

predominance of overflow during snowmelt runoff 

favors the potential for discharge of part of the influent 

nitrogen load delivered by snowmelt runoff. However, 

the large central basin of Flathead Lake and the long 

distance between the lake's primary tributary and outlet 

(fig. 3) are likely to hinder advective transport through 

the lake, especially during periods of low inflow. The 

lake's large surface area also favors trapping of nitrogen delivered by atmospheric deposition, especially 

when such deposition occurs in conjunction with minimal advective transport within the lake. During the 

period analyzed, atmospheric deposition accounted for 

about 11 percent of the total nitrogen input to the lake 

(Stanford and others, 1983).

In addition to physical processes, differences in 

partitioning between bioavailable and particulate nitrogen for both the epilimnion and hypolimnion (fig. 5) 

and input and output loads (fig. 6) indicate that chemical and biological processes affected the in-lake fate 

and transport of nitrogen delivered to the lake. The 

lake's moderate depth, in conjunction with long distances for effective width and length, allows full-depth 

convective mixing of nitrogen (nitrite plus nitrate) during periods without thermal stratification (Stanford and 

others, 1997). When such mixing is coincident with 

advective transport, then part of the lake's nitrogen 

could be discharged. However, the lake's ability to discharge convectively circulated nitrogen is hampered by 

its physical characteristics of long hydraulic residence 

time, moderate depths, and large surface area.

Of these three lakes, Flathead Lake retained the 

largest proportion of its input load of total phosphorus, 

about 75 percent (table 9). Comparable to total nitrogen, about 60 percent of the input load of total phosphorus was delivered to the lake during April through

Fate and Transport of Nutrient Loads 39
June, the period of snowmelt runoff (Stanford and others, 1997). The retention of phosphorus resulted from a 

combination of physical, chemical, and biological processes. Ample evidence demonstrates that Flathead 

Lake is an efficient trap for particulate matter, including particulate phosphorus. The spatial distribution of 

mean annual concentrations of total phosphorus (vertically integrated data) in Flathead Lake from its inlet 

area to its outlet illustrates the lake's ability to retain 

phosphorus (Stanford and others, 1983). On the basis 

of data from 1977-80, the average annual concentration at the inlet was 15 |ig/L; 7.5 km south, at limnological station 1 (fig. 3), the concentration had declined 

to 9 |ig/L. At limnological station 2 (fig. 3), 23 km 

south of the inlet, the concentration had declined to 

about 7.5 |ig/L, which was comparable to the concentration at the lake outlet. Additionally, Stuart (1983) 

presented a mass balance budget for total suspended 

solids (which include sediment-associated phosphorus) 

in Flathead Lake for 1977-79. Of the 292,000,000 kg 

of suspended solids input to the lake, less than 4 percent was discharged from the lake. Lakebed sediment 

analyses for Flathead Lake also clearly indicate that 

sedimentation of total phosphorus occurs; the mean 

concentration of total phosphorus from 70 surficial 

lakebed samples was about 2,300 mg/kg (Moore and 

others, 1982). That concentration was substantially 

larger than the mean concentration of 940 mg/kg noted 

previously for Coeur d'Alene Lake.

Given the substantial sedimentation of particulate 

phosphorus, in conjunction with minimal changes in 

nutrient partioning between inflow and outflow loads 

(fig. 6), some of the bioavailable phosphorus must have 

been converted into particulate phosphorus by the 

chemical process of adsorption and the biological process of phytoplankton assimilation. As discussed previously, phytoplankton assimilation of bioavailable phosphorus was readily evident from time-series data for 

upper water-column concentrations of dissolved orthophosphorus (Stanford and others, 1997). Similar to 

Coeur d'Alene Lake, Flathead Lake also contains ironrich lakebed sediments; the mean concentration of total 

iron measured in 70 surficial lakebed samples was 

44,200 mg/kg (Moore and others, 1982). The presence 

of these iron-rich sediments indicates that adsorption of 

bioavailable phosphorus to iron oxides and hydroxides 

may be an important chemical process favoring the 

lake's retention of phosphorus.

Lake Pend Oreille

Lake Pend Oreille was the outlier among these 

three lakes with regard to the fate and transport of its 

input loads of nitrogen and phosphorus. Input and output loads for Lake Pend Oreille were the largest, as 

were hydraulic residence time, trap efficiency, and both 

mean and maximum depths. However, the percentage 

of retained nitrogen was only slightly larger than that of 

Coeur d'Alene Lake, and the percentage of retained 

phosphorus was the smallest among the three lakes.

The small retention of total nitrogen for Lake 

Pend Oreille, about 15 percent for water years 1989 

and 1990 (table 9), can be attributed primarily to a 

combination of physical limnological processes; chemical and biological processes apparently were less 

important. About 80 percent of the lake's annual load 

of total nitrogen was delivered by the Clark Fork and, 

on the basis of graphical output from the load model 

FLUX, about one-half of that load was delivered during 

April through June, the period of snowmelt runoff. 

During snowmelt runoff, two physical processes were 

likely to have routed most of the influent nitrogen load 

through the lake's northern basin: the coincident occurrence of inflow-plume routing as overflow and the postulated presence of a thermal bar between the lake's 

deep southern basin and its shallow northern basin. The 

role of sedimentation of nitrogen in the lake could not 

be evaluated because of an absence of nutrient data for 

lakebed sediments.

Because of the lake's large values for hydraulic 

residence time, trap efficiency, and depth, and the propensity for phosphorus to sorb to inorganic and organic 

materials, it is logical to expect that Lake Pend Oreille 

would retain a substantial part of its input load of total 

phosphorus. However, the lake retained less than about 

17 percent of the input load of total phosphorus (table 

9). Similar to nitrogen, retention of total phosphorus 

was largely the result of physical limnological processes related to inflow-plume timing and routing 

within the lake, rather than to chemical and biological 

processes. Graphical output from the load model 

FLUX indicates that the Clark Fork, which delivered 

about 70 percent of the lake's annual load of total phosphorus, delivered about one-half of that load during 

April through June, the period of snowmelt runoff. 

Similar to nitrogen, most of the phosphorus load was 

routed through the lake's northern basin by the combination of inflow-plume routing as overflow and the 

postulated presence of a thermal bar between the lake's

40 Fate and Transport of Nitrogen and Phosphorus, Coeur d'Alene Lake, Lake Pend Oreille, and Flathead Lake
deep southern basin and its shallow northern basin. 

Unlike Coeur d'Alene and Flathead Lakes, the adsorption of bioavailable phosphorus to iron oxides and 

hydroxides apparently played a minimal role in retention of phosphorus in Lake Pend Oreille. Surflcial lakebed samples from the outlet arm of Lake Pend Oreille 

contained a mean concentration of 28,500 mg/kg of 

total iron (G.M. Clark, U.S. Geological Survey, written 

commun., 2002), about one-half of the mean concentrations of iron in the other two lakes. Evaluation of 

long-term sedimentation as an indicator of retention 

was not possible because lakebed sediment analyses for 

phosphorus were not available.

SUMMARY AND CONCLUSIONS

The purpose of this report was to describe the role 

of limnological processes in determining the fate and 

transport of nutrients delivered into and discharged 

from Coeur d'Alene and Flathead Lakes and Lake Pend 

Oreille. These three large, natural lakes within the 

NROK study area represented a broad range in physical 

limnological characteristics that could be expected to 

exert substantial influences upon the fate and transport 

of nutrients delivered into them. The large amount of 

limnological and riverine loading data historically 

available for these lakes was used to evaluate how 

interaction among physical, chemical, and biological 

processes within each lake produced quantitative differences between inflow and outflow loads of nutrients.

The outcome of these interactions over a wide 

range of spatial and temporal scales determines the 

quantity and nature of nutrients discharged from each 

lake at its surface-water outlet. Each lake discharged a 

smaller nutrient load than it received; retentions of 

nitrogen loads tended to be smaller than retentions of 

phosphorus loads. Coeur d'Alene Lake, which received 

and discharged the smallest nutrient loads among the 

three lakes, retained about 8 percent and 50 percent, 

respectively, of its input loads of nitrogen and phosphorus. Flathead Lake retained about one-third of its input 

load of nitrogen and about three-fourths of its input 

load of phosphorus. Unlike the other two lakes, Lake 

Pend Oreille retained only about 15 percent of its input 

load of nitrogen and less than about 17 percent of its 

input load of phosphorus; among the three lakes, it 

received and discharged the largest nutrient loads.

In general, the role of physical limnological processes such as circulation and sedimentation accounted

for much of the measured differences in the retention of 

nutrients among the three lakes. Because of its small 

propensity to sorb to inorganic and organic particles, 

nitrogen was less prone to sedimentation and was more 

responsive to advective circulation. Accordingly, the 

retention of nitrogen among the three lakes ranged 

from 5.6 to 36 percent. In contrast, the retention of 

phosphorus among the three lakes ranged from 13.5 to 

75.5 percent, reflecting its strong propensity to sorb to 

inorganic and organic particles. Comparisons of nutrient partitioning between bioavailable and particulate 

fractions in the epilimnia and hypolimnia, as well as in 

input and output loads, provided evidence that chemical and biological processes such as adsorption, remineralization, and phytoplankton assimilation 

affected the quantity and form of nutrients ultimately 

discharged from the lakes.

Limnological processes were evaluated retrospectively and, therefore, required a fair degree of postulation about the interactions among physical, chemical, 

and biological processes because past studies of these 

lakes were more descriptive than process oriented. One 

aim of such postulation was to identify important limnological characteristics that might be incorporated 

into future studies of lakes and reservoirs. For example, 

the postulated existence of a thermal bar in Lake Pend 

Oreille and its role in that lake's small retention of 

nutrients indicates the importance of delineating physical processes related to inflow-plume routing, overall 

lake circulation, and convective circulation. The importance of also addressing chemical and biological processes can be illustrated with the following example 

from Flathead Lake: The substantial sedimentation of 

particulate phosphorus within Flathead Lake, coupled 

with the lack of changes in partitioning between bioavailable and particulate phosphorus in input and output loads, indicate that part of the input load of bioavailable phosphorus was converted into particulate 

phosphorus by the chemical process of adsorption and 

the biological process of phytoplankton assimilation.

Empirical relations were combined with extensive 

historical data to evaluate the role of limnological processes in the fate and transport of nutrient loads in 

these three lakes. If this evaluation had been undertaken with a purely empirical approach and without 

knowledge of historical inflow and outflow nutrient 

loads, the results would not have correctly predicted 

these lakes' nutrient retention. Using variables such as 

areal water load, hydraulic residence time, trap efficiency, and mean depth, the empirical approach likely

Summary and Conclusions 41
would have predicted that the magnitude of nutrient 

retention would progress from small in Coeur d'Alene 

Lake to large in Flathead Lake and Lake Pend Oreille. 

That prediction would be correct only for Flathead 

Lake. If the empirical approach were augmented with 

knowledge of nutrient loads, then the major discrepancy between predicted and measured nutrient retention would become evident for two of the lakes. 

Namely, Lake Pend Oreille deviated sharply from its 

predicted large retention of nutrients and Coeur 

d'Alene Lake retained about one-half of its phosphorus 

input.

This evaluation of the role of limnological processes in the fate and transport of nutrients delivered 

into and discharged from three large, natural lakes 

within the NROK study area provides an example of 

the enhanced scientific understanding to be gained if 

lakes and reservoirs were incorporated into basin-scale 

national water assessments. For example, in a report 

evaluating the NAWQA Program, the National 

Research Council (2002) stated that, "In terms of scientific understanding and management capability, the 

exclusion of lakes and reservoirs precludes an opportunity to understand significant physical, chemical, and 

biological processes that alter water quality." Data 

acquisition programs designed with the capability to 

unravel the interplay of physical, chemical, and biological processes would benefit future limnological studies 

of the fate and transport of constituents, whether initiated by the NAWQA Program or other entities.

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Woods, P.P.—Fate and Transport of Nitrogen and Phosphorus.Coeur d'Alene Lake and Lake Pend Oreille, Idaho, and Flathead Lake, Montana—

U.S. Geological Survey Professional Paper 1682

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