Simulation of Ground-Water Flow in the

Cedar River Alluvial Aquifer Flow System,

Cedar Rapids, Iowa

Scientific Investigations Report 2004-5130

Prepared in cooperation with the City of Cedar Rapids

U.S. Department of the Interior

U.S. Geological Survey

Simulation of Ground-Water Flow in the 

Cedar River Alluvial Aquifer Flow System, 

Cedar Rapids, Iowa

By Michael J. Turco and Robert C. Buchmiller

U.S. Department of the Interior

U.S. Geological Survey

Prepared in cooperation with the City of Cedar Rapids

Scientific Investigations Report 2004-5130
U.S. Department of the Interior

Gale A. Norton, Secretary

U.S. Geological Survey

Charles G. Groat, Director

U.S. Geological Survey, Reston, Virginia: 2004

For sale by U.S. Geological Survey, Information Services

Box 25286, Denver Federal Center

Denver, CO 80225

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

endorsement by the U.S. Government.

Although this report is in the public domain, permission must be secured from the individual copyright owners to reproduce any copyrighted materials contained within this report.

Suggested citation:

Turco, M.J., and Buchmiller, R.C., 2004, Simulation of ground-water flow in the Cedar River alluvial aquifer flow system, 

Cedar Rapids, Iowa: U.S. Geological Survey Scientific Investigations Report 2004-5130, 39 p.
 iii

Contents

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

Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1

Purpose and Scope . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3

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

Acknowledgments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3

Methods of Investigation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3

Surface-Water Measurements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5

Well Construction and Nomenclature . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5

Ground-Water Measurements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5

Aquifer Properties . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5

Hydrogeology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5

Geology and Water-Bearing Characteristics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5

Surface Water . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10

Ground Water . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13

Simulation of Ground-Water Flow . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13

Model Description and Boundary Conditions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13

Model Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16

Model Calibration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22

Steady-State Calibration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23

Transient Calibration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23

Sensitivity Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28

Model Limitations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33

Steady-State Results and Hypothetical Pumping Scenarios . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33

Transient Results and Hypothetical Pumping Scenarios . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36

Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37

References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38

Figures

1-4. Maps showing:

1. Location of study area and surface-water data-collection sites, extent of

digital model, and location of generalized sections through the modeled

area near Cedar Rapids, Iowa . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .2

2. Location of wells used in the modeled area and potentiometric surface of the

Cedar River alluvial aquifer near Cedar Rapids, Iowa, December 21, 1998 . . . . . . . . . .4

3. Thickness of the Cedar River alluvium and adjacent Quaternary deposits

in the modeled area near Cedar Rapids, Iowa . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .11

4. Altitude and configuration of the bedrock surface in the modeled area

near Cedar Rapids, Iowa . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .12

5. Generalized model sections A-A’ and B-B’ based on ground-water flow

model layer construction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .15
iv 

6-10. Maps showing:

6. Extent of modeled area and horizontal hydraulic conductivity in model layer 1. . . . . 17

7. Extent of modeled area and horizontal hydraulic conductivity in model layer 2. . . . . 18

8. Extent of modeled area and horizontal hydraulic conductivity in model layer 3. . . . . 19

9. Extent of modeled area and horizontal hydraulic conductivity in model layer 4. . . . . 20

10. Extent of modeled area and horizontal hydraulic conductivity in model layer 5. . . . . 21

11. Hydrograph showing river stage at Cedar River at Cedar Rapids, Iowa, gaging

station, February 6, 1998, to March 16, 1998. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22

12. Graph of precipitation and snow cover at the Eastern Iowa Airport near

Cedar Rapids, Iowa, and corresponding recharge multiplier for each

transient model stress period . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28

13. Graph showing simulated water levels in layer 2 compared to measured water

levels in layer 2 for observation wells (A) CRM11, (B) CRM12, (C) CRM18,

February 6, 1998, to March 16, 1998 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32

14. Map of simulated potentiometric surface of model layer 2 near Cedar Rapids, Iowa,

under steady-state conditions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34

15. Graph showing pumpage and river inflow for transient model scenarios. . . . . . . . . . . . . . . 36

Tables

1. Statistical summary of measured water levels in observation wells near

Cedar Rapids, Iowa, 1997-99 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6

2. Construction information and estimated hydrologic properties for municipal

water wells near Cedar Rapids, Iowa . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .7

3. Hydrogeologic units in the study area, water-bearing characteristics, and lithology . . . . . 9

4. Values of hydraulic conductivity and storage used for the various hydrogeologic

units in the study area. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14

5. Municipal pumpage rates used in the transient ground-water flow

model calibration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24

6. Cedar River stage during the transient ground-water simulation and incremental

adjustment factor used in the transient river package.. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27

7. Difference between measured and simulated water levels in selected wells within

the study area, February 6, 1998, to March 16, 1998 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29

8. Sensitivity analysis results for each model parameter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31

9. Water budgets for hypothetical steady-state pumping scenarios . . . . . . . . . . . . . . . . . . . . . 35
 v

Conversion Factors and Datum

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

(NAVD 88). Elevation as used in this report refers to distance above or below NAVD 88. NAVD 88 

can be converted to National Geodetic Vertical Datum of 1929 (NGVD 29) by using the National 

Geodetic Survey conversion utility available at URL 

http://www.ngs.noaa.gov/TOOLS/Vertcon/vertcon.html

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

Multiply By To obtain

cubic foot per day (ft3/d) 0.02832 cubic meter per day

cubic foot per second (ft3/s) 0.02832 cubic meter per second

foot (ft) 0.3048 meter

foot per day (ft/d) 0.3048 meter per day

foot squared per day (ft2/d) 0.09290 meter squared per day

gallon per minute (gal/min) 0.06309 liter per second

gallon per minute per foot [(gal/min)/ft)] 0.2070 liter per second per meter

inch (in.) 2.54 centimeter

inch per year (in/yr) 25.4 millimeter per year

mile (mi) 1.609 kilometer

square mile (mi2) 2.590 square kilometer

Simulation of Ground-Water Flow in the Cedar River

Alluvial Aquifer Flow System, Cedar Rapids, Iowa

By Michael J. Turco and Robert C. Buchmiller

Abstract

The Cedar River alluvial aquifer is the primary source of 

municipal water in the Cedar Rapids, Iowa, area. Since 1992, 

the U.S. Geological Survey, in cooperation with the City of 

Cedar Rapids, has investigated the hydrogeology and water 

quality of the Cedar River alluvial aquifer. This report describes 

a detailed analysis of the ground-water flow system in the alluvial aquifer, particularly near well field areas. 

The ground-water flow system in the Cedar Rapids area 

consists of two main components, the unconsolidated Quaternary deposits and the underlying carbonate bedrock that has a 

variable fracture density. Quaternary deposits consist of eolian 

sand, loess, alluvium, and glacial till. Devonian and Silurian 

bedrock aquifers overlie the Maquoketa Shale (Formation) of 

Ordovician age, a regional confining unit.

Ground-water and surface-water data were collected 

during the study to better define the hydrogeology of the Cedar 

River alluvial aquifer and Devonian and Silurian aquifers. 

Stream stage and discharge, ground-water levels, and estimates 

of aquifer hydraulic properties were used to develop a conceptual ground-water flow model and to construct and calibrate a 

model of the flow system. This model was used to quantify the 

movement of water between the various components of the 

alluvial aquifer flow system and provide an improved understanding of the hydrology of the alluvial aquifer.

Ground-water flow was simulated for the Cedar River 

alluvial aquifer and the Devonian and Silurian aquifers using 

the three-dimensional finite-difference ground-water flow 

model MODFLOW. The model was discretized into 223 rows 

and 354 columns of cells. Areal cell sizes range from about 

50 feet on a side near the Cedar River and the Cedar Rapids 

municipal wells to 1,500 feet on a side near the model boundaries and farthest away from the Cedar Rapids municipal well 

fields. The model is separated into five layers to account for the 

various hydrogeologic units in the model area.

Model results indicate that the primary sources of inflow 

to the modeled area are infiltration from the Cedar River 

(53.0 percent) and regional flow in the glacial and bedrock 

materials (34.1 percent). The primary sources of outflow from 

the modeled area are discharge to the Cedar River (45.4 percent) and pumpage (44.8 percent). Current steady-state pumping rates have increased the flow of water from the Cedar River 

to the alluvial aquifer by 43.8 cubic feet per second. Steadystate and transient hypothetical pumpage scenarios were used to 

show the relation between changes in pumpage and changes in 

infiltration of water from the Cedar River. Results indicate that 

more than 99 percent of the water discharging from municipal 

wells infiltrates from the Cedar River, that the time required for 

induced river recharge to equilibrate with municipal pumpage 

may be 150 days or more, and that ground-water availability 

in the Cedar Rapids area will not be significantly affected by 

doubling current pumpage as long as there is sufficient flow in 

the Cedar River to provide recharge.

Introduction

The Cedar River alluvial aquifer is a primary source of 

municipal water in the Cedar Rapids, Iowa, area. The City of 

Cedar Rapids withdraws water for municipal needs from the 

alluvial aquifer adjacent to the Cedar River in Linn County, in 

east-central Iowa (fig. 1). Fifty-three vertical and two horizontal collector municipal wells are located along a reach of the 

Cedar River that extends from near Palo, Iowa, south to Cedar 

Rapids. The Cedar River alluvial aquifer is the only unconsolidated aquifer in the area capable of supplying large quantities of 

water for public and industrial use.

Since 1992, the U.S. Geological Survey (USGS), in cooperation with the City of Cedar Rapids, has investigated the 

hydrogeology and water quality of the Cedar River alluvial 

aquifer. The studies have expanded the knowledge of surfacewater and ground-water interactions in the Cedar River valley 

and their effects on the quality of the ground-water withdrawn 

for municipal supply.

In 1994, the nature of this interaction was evaluated by 

sampling the adjacent alluvial aquifer for biogenic material 

that infiltrates from the Cedar River and monitoring for 

selected water-quality constituents to determine the effectiveness of the alluvial aquifer to filter river-borne biogenic material (Schulmeyer, 1995). Travel times of water from the Cedar 

River to municipal wells were estimated to range from 7 to 

10 days based on changes in water-quality indicators. 

A regional ground-water flow model was constructed in 

the mid-1990’s to simulate ground-water flow in the Cedar 

River alluvial aquifer, the Devonian aquifer, and Silurian 
2 Simulation of Ground-Water Flow in the Cedar River Alluvial Aquifer Flow System, Cedar Rapids, Iowa

Figure 1. Location of study area and surface-water data-collection sites, extent of digital model, and location of generalized sections 

through the modeled area near Cedar Rapids, Iowa.

River

Cedar

30

380

A‘

A

B

A‘

B‘

A

B

A‘

B‘

Linn

County

Linn

County

Study

area

42o

04’

42o

41o

56’

91o48’ 91o44’ 91o40’

Base from U.S. Geological Survey digital data, 1:100,000, 1995

Universal Transverse Mercator projection, Zone 15

North American Datum of 1983

0 1 2 3 MILES

0 1 2 3 KILOMETERS

EXPLANATION

Model boundary

Model section (see figure 5)

Surface-water measurement location

A

Cedar Rapids Cedar Rapids edar Rapids

Palo

Cedar River at Cedar Rapids, IA edar River at Cedar Rapids, IA

Station number 05464500 Station number 05464500

Cedar River near Palo, IA Cedar River near Palo, IA

Cedar River at Cedar Rapids, IA

Station number 05464500

Cedar River near Palo, IA

East well field East well field

West well field West well field

Seminole well field Seminole well field

Low-head dam Low-head dam

East well field

West well field

Seminole well field

Low-head dam

IOWA
Methods of Investigation 3

aquifer over a 231-mi2 area in Benton and Linn Counties near 

Cedar Rapids (Schulmeyer and Schnoebelen, 1998). The 

primary sources of inflow to the regional model included infiltration of precipitation and water from the Cedar River to the 

alluvial aquifer (Schulmeyer and Schnoebelen, 1998). Municipal pumpage accounted for most of the outflow (Schulmeyer 

and Schnoebelen, 1998). Simulation results, assuming hypothetical climate and water-use conditions, indicated that the 

interaction of the Cedar River and the adjacent alluvium was 

more dependent on the total amount of pumpage from the 

system than the amount of infiltration of precipitation. Since 

1999, efforts have been underway to refine the analysis of the 

interaction between the alluvial aquifer and the Cedar River and 

to focus specifically on the three Cedar Rapids well field areas.

Purpose and Scope

This report presents the results of a simulation of groundwater flow in the Cedar River alluvial aquifer and underlying 

bedrock aquifers in the area where municipal water withdrawals 

occur (alluvial aquifer flow system). The report details the construction of a three-dimensional steady-state and transient 

ground-water flow model to provide quantitative estimates of 

the interaction between the alluvial aquifer and the Cedar River 

and provides an analysis of simulated hypothetical pumping 

scenarios and the resulting effect on the amount and timing of 

water infiltrating from the Cedar River. The results can be used 

to describe the potential range in temporal and spatial variations 

of surface-water and ground-water interaction in the Cedar 

River alluvium where municipal pumping causes induced 

recharge to the aquifer. 

Description of Study Area

The study area is located in east-central Iowa and encompasses an area of about 45 mi2

 from about Palo, southeast to 

Cedar Rapids, and includes about a 20-mi reach of the Cedar 

River and adjacent unconsolidated deposits (fig. 1). The study 

area consists of a relatively flat alluvial valley bounded by 

upland areas. Upland areas in the southeastern half of the study 

area include steep bluffs with bedrock exposures and incised 

tributary streams near the Cedar River. The bluffs rise to about 

200 ft above the river floodplain. Upland areas in the northwest 

half of the area consist of lower relief topography. The alluvial 

valley consists primarily of fluvial and glaciofluvial sand and 

gravel deposits, whereas the upland areas consist primarily of 

loess and glacial till. Alluvial deposits, about 100 ft thick, consist primarily of sand and gravel on the inside of river channel 

bends.

The Cedar River flows predominately from northwest to 

southeast through the alluvial valley in the central part of the 

study area. A low-head dam located beneath the Interstate 380 

bridge in Cedar Rapids (fig. 1) maintains river stages in the 

reach adjacent to the most downstream municipal wells during 

periods of low streamflow. Former river-channel meanders, 

sloughs, and oxbow lakes are present as wetland areas, particularly in the upper half of the study area. The Cedar River is in 

direct hydraulic connection with the Cedar River alluvial aquifer. Most pumpage from the Cedar River alluvial aquifer near 

Cedar Rapids occurs along about 6 mi of alluvium upstream 

from the low-head dam at depths ranging from about 40 to 72 ft.

The three Cedar Rapids municipal well fields are located 

primarily north and east of the Cedar River (fig. 2). The Seminole well field (fig. 2) consists of 23 production wells in the 

floodplain. The West well field, located just downstream from 

the Seminole well field, consists of 11 production wells. The 

East well field, located just downstream from the West well 

field, includes 19 production wells. Two horizontal collector 

wells (RANEY1, RANEY2) are located southwest across the 

Cedar River from the Seminole well field (fig. 2).

Land use in much of the northwestern part of the study area 

is agricultural, mostly corn and soybeans (U.S. Department of 

Agriculture, 1976). Land use becomes increasingly urban 

towards the southeastern part of the study area. Riparian areas 

throughout the study area, as well as areas of steeper topography in the southeastern part of the study area, are forested.

Annual precipitation for 1961-90, at the Eastern Iowa airport (not shown in fig. 1) about 8 mi southwest of the well 

fields, averages about 36.39 in/yr (National Oceanic and Atmospheric Administration, 1999). Average annual temperature at 

Cedar Rapids is 49.1oF.

Acknowledgments

The authors would like to thank the personnel of the Cedar 

Rapids Water Department for their assistance in data collection 

and construction of observation wells, G. Ludvigson of the 

Iowa Department of Natural Resources, Iowa Geological 

Survey, for the use of geological maps of Linn County, and the 

numerous USGS field personnel that collected surface-water 

and ground-water data throughout this study. The authors also 

thank Mark Savoca and Dan Christiansen, USGS, for their help 

in converting the conceptual flow model to the digital model 

and preparing data visualizations.

Methods of Investigation

Surface-water and ground-water data were collected 

during this study to better define the hydrogeology of the Cedar 

River alluvial aquifer and Devonian and Silurian aquifers, and 

to assist in construction of the ground-water flow model. Data 

were collected at three surface-water sites along the Cedar 

River and 23 drilled observation wells screened in the Cedar 

River alluvium. Wells used for this study were selected on the 

basis of their location and aquifer completion, with an emphasis 

on a spatial distribution that would adequately represent the 

ground-water flow system at varying distances from the Cedar 

River in the Cedar River alluvial aquifer near the municipal well 

fields.
4 Simulation of Ground-Water Flow in the Cedar River Alluvial Aquifer Flow System, Cedar Rapids, Iowa

Figure 2. Location of wells used in the modeled area and potentiometric surface of the Cedar River alluvial aquifer near Cedar Rapids, 

Iowa, December 21, 1998 (area shown in figure 1).

718

716

714

715

712

715

712

714

716

717

717

719

720

720

718

718

719

718

720

718

"

" "

"

"

""

"

"

"

"

" "" "

"

"

"

"

""

#

##

#

#

#

#

#

#

##

#

#

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#

#

#

#

#

#

#

#

#

#

#

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#

#

#

# #

#

# #

#

#

#

# # #

#

#

#

#

#

#

#

#

#

# #

# #

S23 # #

S22

S21

S20

S19

S15

S16

S14

S13

S12

S17

S18

S10

S9

S8

S7

S6

S5

S4

S3

S11 S2

S1 W8

W7 W11

W6

W10

W5

W9

W4

W3

W2

W1

RANEY1

RANEY2

CRM15

CRM14

CRM16

CRM28

CRM17

CRM19

CRM18

CRM20

CRM21

CRM3 CRM4

CRM6

CRM27

CRM25

CRM23

CRM24

CRM22

CRM26

CRM9

CRM10

CRM7

CRM11

CRM2

CRM1

CRM12

E20

E19 E18

E17 E16

E15 E14

E13 E5

E12

E11

E4 E3

E2 E1 E10

E9

E8

E6

River

Cedar

EXPLANATION

0 0.5 1 Mile

0 0.5 1 Kilometer

East well field East well field

West well field West well field

Seminole well field Seminole well field

East well field

West well field

Seminole well field

41°

59’

42°

01’

91°45' 43' 91°42' 44'

42°

Potentiometric contour—Shows altitude at which water would have

 stood in tightly cased well. Contour interval is 1 foot. Datum is

 NAVD 88. Dashed where approximately located

Observation well and well number

Well fields

Municipal well and well number

CRM23

S10

Base from U.S. Geological Survey digital data, 1:100,000, 1995

Universal Transverse Mercator projection, Zone 15

North American Datum of 1983

Cedar Rapids Cedar Rapids edar Rapids
Hydrogeology 5

Ground-water flow in the study area was simulated using 

the USGS three-dimensional finite-difference ground-water 

flow model MODFLOW (Harbaugh and McDonald, 1996). 

Model parameters interpolated into the finite-difference grid 

and simulation results were processed using the U.S. Department of Defense’s Groundwater Modeling System (GMS) 

(Brigham Young University, 1998). The model was used to 

obtain a better understanding of ground-water flow in the Cedar 

River alluvial aquifer, to provide a quantitative estimate of the 

water budget in the study area, and to evaluate the effect of 

several hypothetical pumping scenarios on the variability of 

surface-water and ground-water interaction in the study area.

Surface-Water Measurements

Streamflow and stage data have been collected periodically from 1902 to 2003 at the USGS streamflow-gaging station 

Cedar River at Cedar Rapids (05464500) (fig. 1) as part of the 

USGS streamflow network in Iowa (Nalley and others, 2003). 

Synoptic surface-water discharge measurements for this study 

were made at two additional selected sites along the Cedar 

River near the town of Palo and from the U.S. Highway 30 

bridge (not shown) southeast of Cedar Rapids in November 

2000 during base-flow conditions and in May 2001 during highflow conditions. The synoptic discharge measurements were 

used to identify and evaluate losing or gaining reaches along the 

Cedar River in the study area. Measured streamflow and stage 

data were utilized in the construction and calibration of the 

ground-water flow model.

Well Construction and Nomenclature

Twenty-three observation wells used for this study were 

installed during previous investigations of the Cedar River 

and the Cedar River alluvial aquifer (Schulmeyer, 1995; 

Schulmeyer and Schnoebelen, 1998). Observation wells were 

developed by pumping three or four casing volumes of water to 

assure a representative water level was obtainable (Schulmeyer 

and Schnoebelen, 1998). All observation and municipal wells 

were surveyed for vertical control and referenced to North 

American Vertical Datum of 1988 and location with a combination of Global Positioning System (GPS) and conventional 

surveying techniques (Schulmeyer and Schnoebelen, 1998). 

Observation wells were identified by a local site name 

containing CRM (Cedar Rapids Municipal) as a prefix followed 

by a unique number (for example, CRM7). Further information 

on these wells and the methods of their construction is available 

in Schulmeyer and Schnoebelen (1998).

Ground-Water Measurements

Measured ground-water levels (table 1) were used to evaluate the local flow directions in the study area, to evaluate the 

seasonal variation in horizontal and vertical ground-water flow, 

to aid in the development and validation of the conceptual 

ground-water flow model, and to aid in the calibration of the 

steady-state and transient numerical model simulations. Automatic water-level recorders measured water levels every 5 minutes in all 23 observation wells. Periodic ground-water levels 

were manually measured to calibrate and verify automatically 

collected data. Manual ground-water levels were measured 

from 1993 to 2002 using a chalked, graduated steel-tape. 

Aquifer Properties

Specific-capacity data provided by the City of Cedar 

Rapids for municipal wells (table 2) and hydraulic conductivities reported in Schulmeyer and Schnoebelen (1998) were used 

as initial estimates of the hydraulic conductivity of the geologic 

materials in the study area. In this report, hydraulic conductivity 

refers to horizontal hydraulic conductivity unless specifically 

referred to as vertical hydraulic conductivity. 

Hydrogeology

Hydrogeologic units in the study area and their waterbearing characteristics are summarized in table 3. Additional 

hydrogeologic information relevant to the description of the 

conceptual ground-water flow system and the construction of 

the ground-water flow model has been presented in previous 

publications (Schulmeyer, 1995; Schulmeyer and Schnoebelen, 

1998). For a more detailed geologic description of the bedrock 

units in the study area the reader is referred to Horick (1984) 

and Olcott (1992). 

Geology and Water-Bearing Characteristics

A variety of unconsolidated materials and bedrock units 

are in direct hydraulic connection in various stratigraphic combinations throughout the study area. Deposits of Quaternary 

age, ranging in thickness from about 10 to 300 ft in the study 

area, compose a complex surficial-aquifer system. Quaternary 

deposits include: the Cedar River alluvium, tributary stream 

alluvium, eolian sand and loess, buried-channel sand and 

gravel, and fractured and unfractured glacial till. All of these 

lithologies have variable permeability, both vertically and 

horizontally. Limestone of Devonian age forms the uppermost 

bedrock in some parts of the study area, but is not present 

throughout the study area. The Otis and Bertram Formations 

of Devonian age form a local confining unit, separating the 

Devonian and Silurian bedrock units in most of the study area. 

Dolomite of Silurian age underlies the entire study area. The 

Maquoketa Shale (Formation) of Ordovician age, a regional 

confining unit, underlies the Silurian dolomite.

Aquifers in the study area include the Cedar River alluvial 

aquifer, tributary stream alluvial aquifers, a buried-channel 

aquifer, the Devonian aquifer, and the Silurian aquifer.
6 Simulation of Ground-Water Flow in the Cedar River Alluvial Aquifer Flow System, Cedar Rapids, Iowa

Table 1. Statistical summary of measured water levels in observation wells near Cedar Rapids, Iowa, 1997-99.

[NAVD 88, North American Vertical Datum of 1988]

Observation

well number

(fig. 2)

Land-surface 

elevation

(feet above 

NAVD 88)

Minimum 

measured

water level

(feet above 

NAVD 88)

Date of

minimum

water level

Maximum 

measured 

water-level 

elevation

(feet above 

NAVD 88)

Date of 

maximum

water level

Assumed 

steady-state 

water-level 

elevation

(feet above 

NAVD 88)

Date of

steady-state 

water-level 

measurement

CRM1 721.26 695.84 11/14/97 720.95 08/10/98 718.85 12/21/98

CRM2 719.52 708.90 03/03/98 717.15 06/12/98 714.78 12/21/98

CRM3 726.71 710.84 02/13/97 723.81 06/22/98 718.29 12/21/98

CRM4 726.45 710.58 02/13/97 724.47 06/22/98 716.08 12/21/98

CRM7 720.38 716.29 10/29/98 721.25 03/17/97 717.58 12/21/98

CRM9 720.55 717.11 08/14/97 721.24 03/17/97 717.60 12/21/98

CRM10 720.65 717.88 12/21/98 718.00 12/04/98 717.88 12/21/98

CRM11 719.24 710.07 03/04/98 718.56 04/06/98 716.01 12/21/98

CRM12 721.99 695.58 01/26/98 721.30 08/10/98 719.24 12/21/98

CRM14 730.00 717.39 12/21/98 720.03 10/29/98 717.39 12/21/98

CRM15 730.00 715.43 02/13/97 728.44 10/07/98 717.46 12/21/98

CRM16 725.00 704.98 02/13/97 723.09 04/03/98 711.59 12/21/98

CRM17 725.00 708.61 02/21/98 722.80 04/03/98 711.29 12/21/98

CRM18 723.00 703.08 02/14/97 725.27 03/17/97 715.66 12/21/98

CRM19 723.00 701.54 02/14/97 724.03 03/17/97 715.40 12/21/98

CRM21 720.00 710.66 10/29/98 710.66 10/29/98 710.66 10/29/98

CRM22 720.00 716.26 12/21/98 723.00 06/23/98 716.26 12/21/98

CRM23 722.00 718.24 12/04/98 726.50 06/22/98 720.98 12/21/98

CRM24 720.00 714.54 12/21/98 724.42 06/23/98 714.54 12/21/98

CRM25 725.00 719.17 12/21/98 724.76 04/06/98 719.17 12/21/98

CRM26 722.00 718.81 09/28/98 720.28 10/29/98 719.24 12/21/98

CRM27 722.00 717.37 12/21/98 720.78 04/29/98 717.37 12/21/98

CRM28 725.00 706.63 05/18/98 723.00 04/06/98 706.81 12/21/98
Hydrogeology 7

Table 2. Construction information and estimated hydrologic properties for municipal water wells near Cedar Rapids, Iowa.

[ft, feet; in., inches; (gal/min)/ft, gallons per minute per foot; ft2/d, feet squared per day; ft/d, feet per day; NAVD 88, North American Vertical Datum of 1988; 

NR, no record; specific-capacity, transmissivity, and hydraulic-conductivity data from Schulmeyer and Schnoebelen (1998)]

Municipal

well number

(fig. 2)

Land-surface 

elevation

(ft above 

NAVD 88)

Well

depth

(ft)

Diameter

of casing

(in.)

Depth to 

top of

well 

screen

(ft)

Length

of well 

screen

(ft)

Distance to 

surface 

water

1

(ft)

Specific 

capacity 

[(gal/min)/ft]

Transmissivity

(ft2/d)

Hydraulic 

conductivity 

(ft/d)

East well field

E1 728 70.0 30 50.0 20.0 63 21.10 2,706 38.70 

E2 728 72.0 30 52.0 20.0 126 23.70 3,153 43.80 

E3 728 72.0 30 52.0 20.0 400 42.90 6,156 85.50 

E4 728 72.0 30 52.0 20.0 400 51.30 7,362 102.30 

E5 728 71.6 30 51.6 20.0 67 45.70 6,558 91.70 

E6 726 70.0 30 50.0 20.0 80 29.40 4,006 57.20 

E8 724 69.6 30 NR 20.0 80 14.20 1,738 25.00 

E9 725 67.0 30 54.0 13.0 80 28.50 3,884 58.00 

E10 726 67.0 30 52.0 15.0 86 26.10 3,472 51.80 

E11 726 56.5 30 36.5 20.0 36 29.20 3,979 70.40 

E12 724 61.0 30 41.0 20.0 43 50.90 7,304 119.70 

E13 724 61.0 30 41.0 20.0 48 39.10 5,439 89.20 

E14 724 65.0 30 44.5 20.0 53 32.20 4,388 67.50 

E15 724 67.0 30 47.0 20.0 32 75.00 11,467 171.10 

E16 724 69.0 30 49.0 20.0 49 74.20 11,345 164.40 

E17 721 59.0 30 39.0 20.0 62 100.00 15,770 267.30 

E18 721 59.0 30 39.0 20.0 57 96.50 14,754 250.10 

E19 721 57.0 30 37.0 20.0 56 62.20 9,148 160.50 

E20 721 56.0 30 36.0 20.0 52 97.00 17,650 315.20 

West well field

W1 724 64.0 30 34.0 10.0 33 75.00 11,467 179.20 

W2 723 72.2 30 62.2 10.0 68 25.00 3,326 46.10 

W3 723 72.4 30 62.4 10.0 31 12.60 1,543 21.30 

W4 724 69.0 30 54.0 15.0 90 17.80 2,283 33.10 

W5 723 68.0 30 53.0 15.0 132 NR NR NR

W6 723 70.9 30 NR NR 93 39.50 5,597 78.90 

W7 724 51.5 30 36.5 15.0 30 31.30 4,354 84.50 

W8 724 61.8 30 51.8 10.0 30 24.10 3,206 51.90 

W9 724 63.0 30 48.0 15.0 38 122.00 19,240 305.40 
8 Simulation of Ground-Water Flow in the Cedar River Alluvial Aquifer Flow System, Cedar Rapids, Iowa

West well field—Continued

W10 724 67.0 30 52.0 15.0 64 63.60 9,354 139.60 

W11 724 66.0 30 21.0 15.0 67 67.00 10,244 155.20 

Seminole well field

S1 720 64.0 30 53.8 10.2 62 17.80 2,793 43.70 

S2 720 53.9 30 43.9 10.0 38 60.00 10,537 195.50 

S3 720 62.9 30 52.6 10.2 100 68.60 12,482 198.40 

S4 720 54.9 30 34.7 10.2 210 53.10 9,325 169.90 

S5 720 64.0 30 34.7 10.2 42 83.30 15,157 236.80 

S6 721 61.1 30 50.9 10.2 41 62.20 10,923 178.80 

S7 721 63.1 30 52.9 10.2 60 84.20 15,320 242.80 

S8 722 57.3 30 47.1 10.2 116 39.90 6,877 120.00 

S9 724 57.5 30 47.2 10.2 115 60.00 10,537 183.30 

S10 725 68.6 30 58.4 10.2 48 61.70 10,836 158.00 

S11 722 62.0 30 47.0 15.0 235 42.00 6,027 97.20 

S12 724 58.0 30 43.0 15.0 500 31.20 4,251 73.30 

S13 724 61.0 30 46.0 15.0 500 53.80 7,913 129.70 

S14 725 59.0 30 44.0 15.0 800 25.40 3,374 57.20 

S15 727 62.0 30 47.0 15.0 800 43.50 6,242 100.70 

S16 726 65.0 30 50.0 15.0 900 24.80 3,296 50.70 

S17 724 58.0 30 34.0 20.0 63 73.10 11,177 192.70 

S18 724 52.0 30 32.0 20.0 81 NR NR NR

S19 724 40.0 30 28.0 12.0 75 NR NR NR

S20 719 43.0 30 28.0 15.0 52 NR NR NR

S21 716 51.7 30 36.7 15.0 78 NR NR NR

S22 721 57.0 30 42.0 15.0 86 NR NR NR

S23 724 57.0 30 40.0 17.0 70 NR NR NR

1

Lateral distance to surface-water source was measured March 22, 1994.

Table 2. Construction information and estimated hydrologic properties for municipal water wells near Cedar Rapids, Iowa.—Continued

[ft, feet; in., inches; (gal/min)/ft, gallons per minute per foot; ft2/d, feet squared per day; ft/d, feet per day; NAVD 88, North American Vertical Datum of 1988; 

NR, no record; specific-capacity, transmissivity, and hydraulic-conductivity data from Schulmeyer and Schnoebelen (1998)]

Municipal

well number

(fig. 2)

Land-surface 

elevation

(ft above 

NAVD 88)

Well

depth

(ft)

Diameter

of casing

(in.)

Depth to 

top of

well 

screen

(ft)

Length

of well 

screen

(ft)

Distance to 

surface 

water

1

(ft)

Specific 

capacity 

[(gal/min)/ft]

Transmissivity

(ft2

/d)

Hydraulic 

conductivity 

(ft/d)
Hydrogeology 9

Table 3. Hydrogeologic units in the study area, water-bearing characteristics, and lithology.

[gal/min, gallons per minute; <, less than; >, more than]

System1

Estimated 

thickness2

(feet)

Hydrogeologic

unit2 Potential well yield2 Lithology2

Quaternary 5-95 Cedar River alluvial 

aquifer

A major source of water in the Cedar 

Rapids area, well yields can be 

greater than 1,000 gal/min.

Fining upward sequence of gravel and sand 

with minor amounts of silt and clay 

(Schulmeyer and Schnoebelen, 1998).

< 50 Tributary stream 

alluvial aquifers

Not a major source of ground water. Occurs along streambeds of tributaries of the 

Cedar River and is composed of gravel, sand, 

silt, and clay (Schulmeyer and Schnoebelen, 

1998).

10-300 Buried-channel 

aquifer

Not a major source of water to the City 

of Cedar Rapids but may yield a large 

volume of water.

Silt, fine- to coarse-grained sand, and coarsegrained angular gravel (Schulmeyer and 

Schnoebelen, 1998).

1->300 Other Quaternary 

deposits (glacial till, 

loess, eolian sand)

Not a major source of water. Glacial material predominately consists of 

clay (till), silt (loess) and sand (eolian sand) 

(Schulmeyer and Schnoebelen, 1998).

Devonian <1-145 Devonian aquifer In areas where the aquifer is highly 

fractured, the substantial increases 

in secondary permeability may yield 

more than 2,000 gal/min with little 

drawdown.

Fractured limestone that is deeply weathered 

where exposed (Schulmeyer and 

Schnoebelen, 1998).

<1-150 Otis and Bertram 

Formations (local 

confining unit)

Not a major source of water. Limestone, dolomite and interbedded shale 

(Schulmeyer and Schnoebelen, 1998).

Silurian 150-350 Silurian aquifer Well yields can be as low as 10 percent 

of those from the Devonian aquifer.

Dolomite with some chert (Schulmeyer and 

Schnoebelen, 1998).

Ordovician 150-350 Maquoketa 

Formation3 (local 

confining unit)

Not a major source of water. Green dolomitic shale and medium- to coarsegrained dolomite and limestone (Schulmeyer 

and Schnoebelen, 1998).

1System for unconsolidated deposits and formations defined by the Iowa Department of Natural Resources, Iowa Geological Survey.

2

Modified from Horick (1984) and Olcott (1992).

3

Also defined as the “Maquoketa Shale.”

The Cedar River alluvial aquifer consists of Cedar River 

alluvium and varies in thickness from about 5 to 95 ft (Hansen, 

1970). The thickness of the alluvium decreases as distance to 

the Cedar River increases; the thinnest alluvium is adjacent to 

the valley walls. The Cedar River alluvium is composed of 

gravel and sand, with minor amounts of silt and clay. Hansen 

(1970) calculated the approximate transmissivity of the alluvial aquifer to be about 20,000 ft2

/d. Subsequent investigations 

by Schulmeyer (1995) suggest transmissivity ranges from 

about 1,500 to about 19,000 ft2/d using the modified Theis 

equation (Heath, 1987). 

Aquifers associated with tributary stream alluvium and 

localized deposits of loess and eolian sand overlie glacial till 

and are of little importance in the study area and thus will not be 

described in detail. Hydraulic conductivity for the loess and 

eolian-sand deposits is estimated to be approximately 

1.2 x 10-3 ft/d and 2 ft/d, respectively, by Hallberg (1980), or 

a transmissivity of about 2.4 x 10-2 ft/d and 40 ft/d, respectively, assuming a 20-ft thickness. Tributary stream alluvial 

aquifers are present along small streams tributary to the Cedar 

River. An estimated hydraulic conductivity of about 28 ft/d for 

the tributary stream alluvial aquifers is presented in Kunkle 
10 Simulation of Ground-Water Flow in the Cedar River Alluvial Aquifer Flow System, Cedar Rapids, Iowa

(1965), or a transmissivity of about 1,400 ft2/d assuming a 

thickness of 50 ft for this deposit. 

A buried-channel aquifer is located along the northwestern 

border of the model area and is in proximity to the city of Palo 

(figs. 3 and 4). The thickness of the buried-channel aquifer 

ranges from about 10 ft to almost 300 ft. This aquifer is in direct 

hydraulic connection with all three major underlying bedrock 

units and underlies the Cedar River alluvium and glacial-till 

deposits. The aquifer consists primarily of silt, fine- to coarsegrained sand, and coarse gravel. Hansen (1970) reports a yield 

of about 67,000 ft3/d from a well completed in the buriedchannel aquifer.

The unconsolidated material in the upland areas adjacent 

to the alluvial aquifers in the study area is composed predominately of glacial till of Pre-Illinoian age. The till consists 

primarily of clay with discontinuous lenses of silt, sand, and 

gravel with occasional pebbles and boulders (Schulmeyer and 

Schnoebelen, 1998). Thickness of the deposits ranges from 

about 1 ft to more than 300 ft (Hansen, 1970). The hydrogeologic properties of the glacial deposits in the study area are 

described in more detail in Schulmeyer and Schnoebelen 

(1998). The upper part of the till is mostly oxidized and fractured whereas the deeper unweathered till is unoxidized and 

unfractured. Hydraulic conductivities of about 8.5 x 10-3 ft/d 

for the fractured till and 5.7 x 10-5 ft/d for the unfractured till 

have been reported (W. Simpkins, Iowa State University, oral 

commun., 1994 from Schulmeyer and Schnoebelen, 1998).

The Devonian aquifer is composed of bedrock of Devonian age that uncomformably underlies the Quaternary deposits 

and can be exposed at land surface or at depths of up to about 

100 ft. The topography of the bedrock surface indicates that 

substantial weathering has occurred in the study area because 

much of the Devonian rocks have been removed by erosion near 

the Cedar River alluvial and buried-channel aquifer. The thickness of the remaining Devonian bedrock in the study area can 

range from less than 1 ft to about 145 ft. The hydraulic conductivity of the Devonian aquifer varies greatly depending on the 

degree of fracturing, dissolution, and other weathering processes. Hydraulic-conductivity values for the Devonian aquifer 

range from 4 to 294 ft/d (Libra and Hallberg, 1985).

The Otis and Bertram Formations of Devonian age form a 

local confining unit that restricts the vertical flow of water 

between the Devonian and underlying Silurian bedrock. The 

formations consist primarily of limestone, dolomite, and a basal 

shale. Similar to the overlying Devonian bedrock, the Otis and 

Bertram Formations also have been removed in parts of the 

study area. The thickness of the formations can range from less 

than 1 ft to about 150 ft in the study area. Where the Otis or 

Bertram Formation is the uppermost bedrock unit and is weathered, the unit can have the same hydrogeologic properties as the 

overlying Devonian bedrock (Schulmeyer and Schnoebelen, 

1998). 

The Silurian aquifer is composed of bedrock of Silurian 

age and consists of dolomite and is continuous throughout the 

study area (Horick, 1984). The topography of the Silurian 

bedrock indicates little weathering in the study area, with the 

exception of the areas beneath the Cedar River valley and the 

northern part of the buried-channel aquifer (figs. 3 and 4) where 

the Silurian bedrock is the uppermost unit. The thickness of the 

unit in the study area ranges from about 150 to 350 ft. A transmissivity of about 1,349 ft2/d and a hydraulic conductivity of 

about 6.1 ft/d for a well completed in the Silurian aquifer was 

estimated from a pumping test (Hansen, 1970). 

The Maquoketa Shale (Formation) of Ordovician age 

is the lowermost unit in the conceptual model of the flow 

system and is a regional confining unit. This formation consists 

predominately of shale, limestone, and dolomite. This lowpermeability unit restricts the vertical flow of water and is not 

known to yield substantial quantities of water to wells (Hansen, 

1970).

Surface Water

The major surface-water body in the study area is the 

Cedar River. The river has its headwaters in southern Minnesota 

and flows southeasterly to its confluence with the Iowa River in 

southeast Iowa. The Cedar River acts as the regional hydrologic 

control for discharge of the surficial ground-water systems in 

the absence of anthropogenic stresses. In the study area, the 

Cedar River has eroded through and removed all of the glacial 

deposits, the Devonian age bedrock, and most of the Otis and 

Bertram Formations in the vicinity of Cedar Rapids. The annual 

mean daily flow for 1903-99 is 3,760 ft3/s; the highest daily 

flow of 71,500 ft3

/s occurred on March 31, 1961. Historically, 

March and April have greater daily mean flows than other 

months of the year (Nalley and others, 2003). Flow at the Cedar 

River at Cedar Rapids streamflow-gaging station exceeds 

680 ft3

/s 90 percent of the time.

Synoptic surface-water-discharge measurements were 

made at two sites along the Cedar River in the study area on 

November 16, 2000, and May 29, 2001. The November 

measurements showed a loss of streamflow from Palo to the 

Cedar River at Cedar Rapids gage of about 130 ft3

/s, and a 

gain of about 300 ft3

/s for the reach from the gage to U.S. 

Highway 30. The May measurements were made during a 

period of high flow and all reaches were gaining reaches, likely 

due more to tributary stream contributions to the Cedar River 

rather than additional ground-water discharge.

Other surface-water features in the study area include 

oxbow lakes and abandoned channels in the Cedar Rapids well 

field areas created by the historical meandering of the Cedar 

River. The oxbow lakes predominately have fine-grained bed 

material that limits or reduces infiltration into the alluvial 

aquifer. During periods of Cedar River base flow, fine-grained 

material may be deposited on the riverbed upstream from the 

low-head dam, reducing the conductance of the riverbed and 

decreasing the movement of water between the river and the 

alluvial aquifer.
Hydrogeology 11

Figure 3. Thickness of the Cedar River alluvium and adjacent Quaternary deposits in the modeled area near Cedar Rapids, Iowa.

River

Cedar

30

380 42o

04’

42o

41o

56’

91o48’ 91o44’ 91o40’

0 1 2 3 MILES

0 1 2 3 KILOMETERS

EXPLANATION

Buried

Channel

Base from U.S. Geological Survey digital data, 1:100,000, 1995

Universal Transverse Mercator projection, Zone 15

North American Datum of 1983

Thickness, in feet

0 to 50

50 to 100

100 to 150

150 to 200

200 to 250

250 to 300

300 to 350

350 to 400

Cedar Rapids Cedar Rapids edar Rapids

Palo
12 Simulation of Ground-Water Flow in the Cedar River Alluvial Aquifer Flow System, Cedar Rapids, Iowa

Figure 4. Altitude and configuration of the bedrock surface in the modeled area near Cedar Rapids, Iowa.

River

Cedar

30

380

750

750

500

550

600

650

700

700

800

700

600

700

700

700

800

650

650

650

800

800

750

750

750

700

800

750

750

600

600

650

650

700

700

42o

04’

42o

41o

56’

91o48’ 91o44’ 91o40’

0 1 2 3 MILES

0 1 2 3 KILOMETERS

EXPLANATION

Bedrock contour—Shows altitude of bedrock surface.

 Contour interval 50 feet. Vertical datum is NAVD 88

Buried

Channel

Cedar Rapids Cedar Rapids edar Rapids

Palo

Base from U.S. Geological Survey digital data, 1:100,000, 1995

Universal Transverse Mercator projection, Zone 15

North American Datum of 1983
Simulation of Ground-Water Flow 13

Ground Water

The ground-water flow system in the Cedar Rapids area is 

composed of two main components, the unconsolidated Quaternary deposits and the underlying bedrock that has a variable 

fracture density. These two components are in direct hydraulic 

connection throughout the study area and have variable thicknesses and water-bearing characteristics (table 3). The flow 

system is composed of both local and regional flow systems, 

all of which would discharge to the Cedar River under predevelopment conditions.

In the absence of pumpage from the Cedar River alluvial 

aquifer, ground-water flow is typically towards the Cedar River 

and down the Cedar River valley. During periods of rapid stage 

increase in the Cedar River, ground-water flow gradients can be 

temporarily reversed and water flows from the river to the alluvial aquifer. Pumping, as currently occurs in the study area, also 

can reverse the normal direction of ground-water flow in the 

vicinity of the municipal well(s) and induce infiltration from the 

Cedar River to the alluvial aquifer. Drawdown cones surrounding several of the Cedar Rapids municipal wells caused by 

pumpage on December 21, 1998, are shown in figure 2.

Recharge to the alluvial aquifer is from infiltration of 

precipitation and runoff from the upland areas adjacent to the 

alluvial aquifer, infiltration of Cedar River water in areas of 

municipal pumpage, and regional flow from underlying bedrock units. Discharge from the alluvial aquifer is primarily to 

the Cedar River and municipal pumpage.

Ground-water flow in the Devonian and Silurian aquifers 

is primarily regional and is not significantly influenced by local 

conditions. Historically, the two aquifers were considered to be 

hydrogeologically similar and were referred to as the SilurianDevonian aquifer (Horick, 1984). However, recent investigations have shown that the two aquifers have significantly different hydrogeologic properties in many areas. The Devonian 

aquifer, when present as the uppermost bedrock unit, can have 

hydraulic conductivities an order of magnitude larger than the 

Silurian aquifer due to increased secondary permeability, 

primarily fractures enhanced by dissolution (Turco, 2002). 

Recharge to the bedrock aquifers occurs regionally where the 

bedrock is exposed at land surface outside of the study area or 

through vertical flow from overlying Quaternary deposits. The 

Devonian and Silurian aquifers are physically separated in most 

parts of the study area by the confining unit composed of the 

Otis and Bertram Formations. The primary flow direction for 

the two bedrock aquifer systems is towards the Cedar River and 

down the Cedar River valley, much like the overlying Cedar 

River alluvial aquifer. The primary area of discharge for the 

Devonian and Silurian aquifers is the Cedar River alluvial 

aquifer, though there is a regional flow component to the southeast of the study area. The bedrock aquifers are described in 

greater detail in Schulmeyer and Schnoebelen (1998).

Simulation of Ground-Water Flow

Ground-water flow was simulated for the Cedar River 

alluvial aquifer and the Devonian and Silurian aquifers using 

the three-dimensional finite-difference ground-water flow 

model MODFLOW (Harbaugh and McDonald, 1996). MODFLOW can simulate ground-water flow in a three-dimensional 

heterogeneous and anisotropic medium, using a partial differential equation where the partial derivatives represent the movement of water, provided that the principle axes of hydraulic 

conductivity are aligned with the coordinate system (Harbaugh 

and McDonald, 1996). The flow equation was solved using the 

preconditioned conjugate-gradient (PCG2) procedure (Hill, 

1990), a method that allows for both linear and non-linear flow 

conditions.

The flow model was constructed to simulate both steadystate and transient conditions. Steady-state conditions occur 

when the volumetric rate of water entering a system equals the 

volumetric rate of water flowing out of the system. Steady-state 

conditions represent a ground-water flow system that is at equilibrium with a set of constant, specified stresses. Ground-water 

levels measured in December 1998 in the Cedar River alluvial 

aquifer and the Devonian aquifer were considered to be an 

acceptable estimate of steady-state conditions. Ground-water 

levels and streamflow during this time show little variation. No 

water-level measurements were available for the Silurian 

aquifer; however, there are no known significant or varying 

stresses on this aquifer in the study area. The stage of the Cedar 

River was simulated assuming base-flow conditions. Recharge, 

used to account for infiltration of precipitation and evapotranspiration, was assumed to be the average daily recharge to the 

system. 

The transient model was used to simulate changes that 

occur in the ground-water flow system with respect to time, as 

opposed to the steady-state model, which does not specify the 

amount of time required to reach equilibrium. The transient 

model was calibrated using a rise in river stage that occurred 

during the months of February-March 1998. This increase in 

river stage was caused by an increase in air temperature and 

resultant snowmelt. The transient simulations used hypothetical 

pumping scenarios to evaluate the time-dependant effects of 

pumping rates on the movement of water infiltrating the alluvial 

aquifer from the Cedar River. 

Model Description and Boundary Conditions

The MODFLOW model grid covers an area of 45 mi2 and 

simulates ground-water flow through all hydrogeologic units 

described in the “Geology and water-bearing characteristics” 

section. The modeled area is variably discretized into 223 rows 

and 354 columns, with a finer mesh grid near the Cedar Rapids 

municipal wells and larger cell sizes near the outer edges of the 

model (fig. 1). Cells range from about 50 ft to about 1,500 ft on 

a side. The model was constructed using bedrock topology 

developed by the Iowa Department of Natural Resources-Iowa 

Geological Survey.
14 Simulation of Ground-Water Flow in the Cedar River Alluvial Aquifer Flow System, Cedar Rapids, Iowa

Five model layers were used to represent the major hydrogeologic units in the model area (table 4). Hydrogeologic units 

are assigned to specific model layers, based on unconsolidated 

and bedrock lithology, which simplifies the conceptualization 

of the model. Layers 1 and 2 represent the unconsolidated 

deposits. Layer 1 represents the upper 15 ft of the unconsolidated material, which includes loess, eolian sand, fractured 

glacial till, and the uppermost portions of the Cedar River alluvial and buried-channel aquifers. Layer 2 represents the remainder of the fractured and unfractured glacial till in the upland 

areas and includes the lower, coarser grained parts of the Cedar 

River alluvial and buried-channel aquifer. Municipal water 

withdrawals are made from layer 2. The Devonian aquifer, Otis 

and Bertram confining unit, and Silurian aquifer are represented 

in the model as layers 3, 4, and 5, respectively. The approximate 

thickness of the five layers is shown in two generalized sections 

through the modeled area in figure 5. Model layers were simulated as unconfined (layer 1), convertible (layers 2, 3, 4), and 

confined (layer 5). Simulated hydrologic conditions can change 

from unconfined to confined in convertible layers depending on 

the simulated water-table surface.

The model area is limited in size compared to the lateral 

extent of the unconsolidated and bedrock aquifers being investigated. To represent this limitation, model boundary conditions 

are used to account for conceptualized flow from areas beyond 

the extent of the modeled area.

The top of layer 1 is simulated as a “free surface” allowing 

water to enter the system by way of recharge and leave the 

system by way of evapotranspiration. The perimeter of the 

model is bounded by a combination of variable-flux boundaries, 

termed general-head boundaries, and no-flow boundaries. 

Layers 1 and 2 of the model are simulated using no-flow 

boundaries on the northeastern and southwestern margins to 

simulate conceptualized ground-water flow divides associated 

with surface-water basin boundaries, and on the northwestern 

and southeastern margins to simulate conceptualized flow 

parallel to ground-water flow paths towards the Cedar River. 

The boundaries of the bedrock units, layers 3, 4, and 5, are 

simulated with general-head boundaries along the northeastern 

and southwestern margins and with no-flow boundaries along 

the northwestern and southeastern margins. The general-head 

boundaries are based on relative head differences between the 

model cells and the regional potentiometric surface. A constant 

head source is placed 1 mi from the closest active model cell, 

and the hydraulic conductivity of the laterally adjacent unit 

is used in the computation of ground-water flux across the 

boundary. The ground-water level at the boundary was derived 

from simulated heads in the regional model (Schulmeyer and 

Schnoebelen, 1998). The bottom of layer 5, the lowest 

simulated hydrogeologic unit, is simulated as a no-flow boundary associated with the Maquoketa Shale regional-confining 

unit. 

Table 4. Values of hydraulic conductivity and storage used for the various hydrogeologic units in the study area.

[ft/d, feet per day; --, not applicable]

System1 Hydrogeologic

unit Generalized lithology Model 

layer

Horizontal 

hydraulic 

conductivity

(ft/d)

Vertical 

hydraulic 

conductivity

(ft/d)

Specific yield 

(dimensionless)

Specific 

storage

(per foot)

Quaternary 

deposits

Loess, eolian sand Silt, clay 1 10.00 1.00 0.40-0.42 --

Glacial till Fractured, oxidized clay 1, 2 40.00 4.00 0.10 0.0005

Glacial till Unfractured, unoxidized clay 2 4.00 1.00 0.05 0.002

Cedar River 

alluvial aquifer

Silty, fine-grained sand 1 4-100 1-10 0.25 0.0002

Fine- to medium-grained sand 1, 2 170-432 17-43 0.30-0.40 0.00005

Medium- to coarse-grained sand 1, 2 170-600 17-60 0.45 0.00005

Buried channel 

aquifer

Medium- to coarse-grained sand 2 40-500 4-50 0.45 0.00001

Devonian Devonian aquifer Limestone and dolomite 3 0.1-350 0.001-1.0 0.1-0.15 0.00001

Otis-Bertram2 

confining unit

Limestone, dolomite, and shale 4 0.1-350 0.001-.01 0.01-.05 0.00001

Silurian Silurian aquifer Dolomite 5 0.1-10.0 0.001-1.0 0.1-0.15 0.00001

1

System for unconsolidated deposits and formations defined by the Iowa Department of Natural Resources, Iowa Geological Survey.

2For convenience, the Otis Formation and Bertram Formation are combined to form a local confining unit.
Simulation of Ground-Water Flow 15

Figure 5. Generalized model sections A-A’ and B-B’ based on ground-water flow model layer construction. Traces of sections shown 

in figure 1.

A A‘

B B‘

SW NE

NW SE

0 1 2 MILES

0 1 2 KILOMETERS

Cedar

River

Tributary

Stream

VERTICAL SCALE GREATLY EXAGGERATED

Layer 1 Layer 2

Layer 3

Layer 4

Layer 5

Layer 1

Layer 2

Layer 3 Layer 4

Layer 5

Cedar

River

Cedar

River

Interstate

380
16 Simulation of Ground-Water Flow in the Cedar River Alluvial Aquifer Flow System, Cedar Rapids, Iowa

Model Parameters

The ground-water flow model includes large arrays of 

numerical values used to represent the various geometric, 

hydrogeologic, and climatic variables in the model grid. These 

arrays are referred to as parameters, which can be assigned to 

represent rivers, drains, wells, various hydraulic properties, and 

geologic topology. Parameters are assigned to the centroid of 

each model cell and are assumed to be the average value 

throughout the cell. Individual model cells identified as having 

boundary conditions, river, drain, or well parameters assigned 

to them are not shown because of the scale of the model grid for 

this study.

The model was constructed using elevations interpolated 

from available topographic and geologic maps. The elevation of 

land surface was interpolated using a kriging technique from a 

USGS 30-meter digital-elevation model. Relevant geologic 

contacts in the study area were interpolated to the model grid 

using the GMS software by the inverse-distance-weighted 

(IDW) method (Brigham Young University, 1998).

Modeled area orientation and hydraulic-conductivity 

zones for each model layer are shown in figures 6-10. Initial 

hydraulic-conductivity values for the various geologic 

materials were obtained from estimates in Schulmeyer and 

Schnoebelen (1998), which were then modified within appropriate ranges during model calibration to produce the best-fit 

model. Horizontal hydraulic conductivities in the Quaternary 

deposits simulated in layers 1 and 2 ranged from about 4 to 

600 ft/d (table 4). Horizontal hydraulic conductivity in layers 3, 

4, and 5 included the estimated increase in conductivity due to 

secondary permeability near the Cedar River valley. Hydraulic 

conductivities in the Devonian and Silurian bedrock ranged 

from 0.1 to about 350 ft/d (table 4). 

Vertical hydraulic conductivity for the entire model is simulated as a constant factor of one-tenth of the horizontal hydraulic conductivity at each grid cell. Vertical leakance is required 

by the model to control the rate of ground-water flow between 

layers. Vertical leakance between two adjacent layers is calculated from the thickness of each layer between its node and the 

common layer contact and the vertical hydraulic conductivity of 

each layer (McDonald and Harbaugh, 1988). Vertical leakance 

between two model layers with an intervening confining unit is 

calculated from the above properties and the vertical hydraulic 

conductivity and thickness of the confining unit (McDonald and 

Harbaugh, 1988).

Natural stresses on the aquifer system include precipitation, evapotranspiration, changes in streamflow of the Cedar 

River, and drainage from tributary streams in the study area. 

Recharge, in the form of infiltration of precipitation, was simulated in the steady-state and transient ground-water flow model 

using values of approximately 6.0 to 7.8 in/yr as previously 

published by Schulmeyer and Schnoebelen (1998). The rate 

varied depending on the surficial lithology, with larger values in 

the alluvium to reflect an increased capacity for infiltration and 

smaller values in the glacial deposits.

The effects of vegetation on the ground-water flow system 

through evapotranspiration were simulated as a constant value 

throughout the model area. The value of evapotranspiration was 

established during the calibration process to be 0.0095 ft/d for 

the transient simulation. The extinction depth was estimated to 

be 5 ft, which was assumed to be the approximate maximum 

depth of most tree roots in the area, and the surface was the top 

of layer 1. Field measurements of evapotranspiration were not 

recorded during this study because evapotranspiration was not 

assumed to be a significant portion of the total discharge from 

the alluvial aquifer.

The Cedar River in the study area was simulated using 

river cells in the MODFLOW model to allow water to flow into 

and out of the adjacent alluvial aquifer. Flow across a river cell 

in the model occurs through a riverbed conductance term, 

which is a function of the area of the river channel, the vertical 

hydraulic conductivity of the riverbed material, and the thickness of the riverbed (McDonald and Harbaugh, 1988). An estimated river stage was assigned to each model cell using the 

stage of the Cedar River at Cedar Rapids gaging station and 

available topographic data upstream from the low-head dam. 

River stage from the dam upstream to the northern end of the 

Seminole well field near S23 (fig. 2) was held constant at 

718 ft to account for the pool created by the dam. Upstream 

from S23, the river stage was interpolated along the river reach 

using topographic elevation data. The riverbed conductance 

was gradually increased from about 5 ft/d near the dam to 

about 1,000 ft/d near S23 to simulate the effects of riverbed 

siltation behind the dam. The stage of the river was adjusted 

during the transient simulation by applying a daily stage 

increase or decrease to the river cells for each stress period 

(fig. 11) based on streamflow records from the Cedar River at 

Cedar Rapids streamflow-gaging station.

Tributary streams in the model area are simulated as drain 

cells. Drain cells allow water to move out of the ground-water 

flow system across the drain boundary if the head in the adjacent model cell is higher than the specified drain elevation 

(McDonald and Harbaugh, 1988). Drain elevations were estimated from topographic data and elevations were set at about 

5 ft below land surface. Conductance of the drain-bed material 

was estimated to be about 2 ft/d. All drains in the steady-state 

and transient simulations were assigned the same bed-material 

conductance value and were held constant during the transient 

simulation.

Municipal wells in the study area are simulated using the 

WELL package (Harbaugh and McDonald, 1996). The design 

of the model grid ensures that each municipal well is located at 

the centroid of a cell in layer 2. The lateral collector wells, 

RANEY1 and RANEY2 (fig. 2), are simulated as numerous 

individual wells, 16 and 19 wells, respectively. The total 

collector well pumpage was evenly distributed to each of the 

individually simulated wells. During the steady-state simulation, 19 of the 53 vertical wells pump at a historical average 

pumping rate of about 1.5 ft3

/s to 2.2 ft3/s, and each collector 

well pumps at about 9.0 ft3

/s for a total withdrawal rate of 

50.6 ft3

/s. However, during the transient calibration simulation, 

wells were turned “off” and “on” over time and have a variable 

pumping rate associated with recorded withdrawal amounts. 
Simulation of Ground-Water Flow 17

Figure 6. Extent of modeled area and horizontal hydraulic conductivity in model layer 1.

River

Cedar

30

380 42o

04’

42o

41o

56’

91o48’ 91o44’ 91o40’

0 1 2 3 MILES

0 1 2 3 KILOMETERS

EXPLANATION

Horizontal hydraulic conductivity, in feet per day,

 and hydrogeologic unit

10, Loess, eolian deposits

40, Glacial till, fractured, oxidized

65, Cedar River alluvium, fine-grained sand

86, Cedar River alluvium, fine- to medium-grained sand

173, Cedar River alluvium, medium- to coarse-grained sand

520, Cedar River alluvium, coarse-grained sand

Cedar Rapids Cedar Rapids edar Rapids

Palo

Base from U.S. Geological Survey digital data, 1:100,000, 1995

Universal Transverse Mercator projection, Zone 15

North American Datum of 1983
18 Simulation of Ground-Water Flow in the Cedar River Alluvial Aquifer Flow System, Cedar Rapids, Iowa

Figure 7. Extent of modeled area and horizontal hydraulic conductivity in model layer 2.

River

Cedar

30

380 42o

04’

42o

41o

56’

91o48’ 91o44’ 91o40’

0 1 2 3 MILES

0 1 2 3 KILOMETERS

EXPLANATION

Horizontal hydraulic conductivity, in feet per day, and hydrogeologic unit

Cedar Rapids Cedar Rapids edar Rapids

Palo

4, Glacial till, unfractured, unoxidized

9, Cedar River alluvium, silty fine-grained sand

40, Glacial till, fractured, oxidized 

65, Cedar River alluvium, fine-grained sand

86, Cedar River alluvium, fine- to medium-grained sand

346, Cedar River alluvium, medium- to coarse-grained sand

432, Cedar River alluvium. medium- to coarse-grained sand

500, Buried-channel aquifer

600, Cedar River alluvium, coarse-grained sand

Base from U.S. Geological Survey digital data, 1:100,000, 1995

Universal Transverse Mercator projection, Zone 15

North American Datum of 1983
Simulation of Ground-Water Flow 19

Figure 8. Extent of modeled area and horizontal hydraulic conductivity in model layer 3.

9, Devonian aquifer, unweathered

44, Devonian aquifer, slightly weathered

350, Devonian aquifer, highly weathered

River

Cedar

30

380 42o

04’

42o

41o

56’

91o48’ 91o44’ 91o40’

0 1 2 3 MILES

0 1 2 3 KILOMETERS

EXPLANATION

Horizontal hydraulic conductivity, in feet per day,

 and hydrogeologic unit

Cedar Rapids Cedar Rapids edar Rapids

Palo

0.1, Devonian confining unit

Base from U.S. Geological Survey digital data, 1:100,000, 1995

Universal Transverse Mercator projection, Zone 15

North American Datum of 1983
20 Simulation of Ground-Water Flow in the Cedar River Alluvial Aquifer Flow System, Cedar Rapids, Iowa

Figure 9. Extent of modeled area and horizontal hydraulic conductivity in model layer 4.

River

Cedar

30

380 42o

04’

42o

41o

56’

91o48’ 91o44’ 91o40’

0 1 2 3 MILES

0 1 2 3 KILOMETERS

EXPLANATION

Horizontal hydraulic conductivity, in feet per day,

 and hydrogeologic unit

Cedar Rapids Cedar Rapids edar Rapids

Palo

350, Otis-Bertram Formation, highly weathered

0.9, Otis-Bertram, Formation, slightly weathered

0.1, Otis-Bertram Formation, unweathered

Base from U.S. Geological Survey digital data, 1:100,000, 1995

Universal Transverse Mercator projection, Zone 15

North American Datum of 1983
Simulation of Ground-Water Flow 21

Figure 10. Extent of modeled area and horizontal hydraulic conductivity in model layer 5.

River

Cedar

30

380 42o

04’

42o

41o

56’

91o48’ 91o44’ 91o40’

0 1 2 3 MILES

0 1 2 3 KILOMETERS

EXPLANATION

Horizontal hydraulic conductivity, in feet per day,

 and hydrogeologic unit

Cedar Rapids Cedar Rapids edar Rapids

Palo

0.1, Silurian aquifer, unweathered

1, Silurian aquifer, slightly weathered

10, Silurian aquifer, weathered

Base from U.S. Geological Survey digital data, 1:100,000, 1995

Universal Transverse Mercator projection, Zone 15

North American Datum of 1983
22 Simulation of Ground-Water Flow in the Cedar River Alluvial Aquifer Flow System, Cedar Rapids, Iowa

Figure 11. Hydrograph showing river stage at Cedar River at Cedar Rapids, Iowa, gaging station, February 6, 1998, to March 16, 1998.

704.0

704.5

705.0

705.5

706.0

706.5

2/62/72/82/9

2/102/112/122/132/142/152/162/172/182/192/202/212/222/232/242/252/262/272/28

3/13/23/33/43/53/63/73/83/9

3/103/113/123/133/143/153/16

DATE

ELEVATION OF RIVER STAGE, IN FEET ABOVE NAVD 88

The transient simulation required additional model parameters not needed for the steady-state simulation. Specific storage was assigned to all model layers, except for layer 1, which 

was specified as unconfined and assigned a specific yield of 

0.40-0.42 ft-1. Specific storage values for the various lithologies 

were estimated from published values by Anderson and 

Woessner (1992) and ranged from 0.002 ft-1 in glacial till to 

0.00001 ft-1 in the bedrock. Specific-yield values were applied 

to all model layers defined as convertible (layers 2, 3, and 4) or 

confined (layer 5) and were estimated from published values 

typical for the various lithologies in the study area (Anderson 

and Woessner, 1992). The simulated specific yield ranged from 

0.01 in the Otis and Bertram Formations to 0.45 in the coarsegrained sand of the buried-channel and Cedar River alluvial 

aquifers. Storage values used for the various geologic materials 

simulated in the ground-water flow model are summarized in 

table 4. 

Model Calibration

The ground-water flow model was calibrated by adjusting 

the value and distribution of model input parameters so that the 

resulting model output matched measured water levels and 

other hydrologic observations within an acceptable level of 

accuracy. Changes to hydrogeologic parameter values were 

evaluated during the calibration process to assure that the 

change implemented was within the acceptable range of variability of the parameter. After each change in model parameter 

value, model output was generated and compared with 

measured data to evaluate the effect of the selected parameter 

change. The model accuracy was calculated using the root mean 

square error (RMSE) (Anderson and Woessner, 1992) comparison between water-level measurements and simulated water 

levels. Model accuracy is increased as RMSE (eq. 1) is 

decreased. Average model error (AVEH) also was used during 

the calibration process to evaluate model bias. Model bias 

occurs when the difference between simulated and observed 

water levels is predominately positive or negative. 

(1)

where:

M is the measured water level;

S is the simulated water level; and

N is the number of observations.

The model was considered calibrated when the following 

criteria were satisfied:

1. Incremental parameter changes in model input did not 

result in a smaller RMSE for model layers 2 and 3, which 

include the Cedar River alluvial aquifer and Devonian 

aquifer, respectively, and an AVEH closer to zero;

RMSE

( ) M S – 2

1

N

∑

N = --------------------------
Simulation of Ground-Water Flow 23

2. The RMSE is less than 2 ft for layers 2 and 3;

3. The simulated ground-water flow directions in the model 

compared favorably with those determined from waterlevel measurements and previously published 

potentiometric surface maps of the Devonian and 

Silurian aquifers;

4. The simulated streamflow loss from the Cedar River to 

the Cedar Rapids well fields compares favorably with the 

estimated base-flow streamflow and measured 

streamflow values for the assumed steady-state time 

period; and

5. The simulated transient water levels and the measured 

water levels during the transient calibration period react 

to the effects of variable stresses through time in a logical 

manner throughout the simulation.

Steady-State Calibration

Steady-state water-level data were obtained during a synoptic measurement on December 21, 1998. The data are considered to be a close approximation of steady-state conditions. It is 

important to note that due to the constant variability in river 

stage, precipitation, and pumpage, the Cedar River alluvial 

aquifer may only reach approximate steady-state conditions for 

limited periods of time.

As the model was constructed, assumptions were necessary to reduce the instability of the model. The model was 

initially simplified, with uniform hydraulic conductivity for 

each model layer and constant riverbed conductance throughout 

the model. As calibration proceeded, complexity was systematically integrated into the model to improve the model output and 

to better represent actual conditions by increasing the variability of hydraulic conductivity, adding pumpage, and adjusting 

other hydrogeologic parameters of the model area to the extent 

supported by the available hydrogeologic data. 

Surface-elevation conflicts between the model layers were 

corrected using the GMS software. The elevation of the bedrock 

contacts was preserved, allowing the other surface elevations to 

change slightly to eliminate overlapping layer surfaces and 

maintain a positive thickness for all model layers.

The extent of dry cells in the model area was monitored 

throughout the calibration process. Dry cells occur during a 

simulation when the head in a cell falls below the bottom elevation of the cell. In the Cedar Rapids area, it is conceptually valid 

that many of the cells in layer 1 and 2 would become dry during 

the simulation due to the small geologic unit thicknesses in the 

upland area and constant 15-ft thickness of layer 1. Dry cells in 

these areas represent a water-table surface that is below the 

bottom of the cell in that layer. Dry cells in the Devonian bedrock are conceptually more problematic, although, their occurrence along the steep elevation change in the bluff areas near the 

river valley is hypothetically valid assuming that these steep 

exposures are well drained and the water table is deeper than the 

Devonian rocks. Model parameters were adjusted to minimize 

the number of dry cells in layers 1 through 3 as indicated by the 

conceptual model. The initial conceptual model assumed that 

layers 2 and 3 were wet throughout the model area; however, 

that assumption was changed during calibration because no 

reasonable parameter value used could produce such a result. 

The RMSE for the calibrated steady-state model was calculated using water-level data from most of the observation 

wells in the model area. Wells CRM23 and CRM28 in the 

Seminole well field (fig. 2) were not used in the calculation 

because of significant differences in water levels compared to 

nearby wells; thus, these water levels were considered to be 

atypical of the alluvium in that area on December 21, 1998. 

Water levels measured in other observation wells near CRM23 

and CRM28 produced a good model fit and appeared to be 

realistic. The RMSE for the calibrated steady-state model is 

1.44 ft; the AVEH is -0.26 ft. The RMSE for the Devonian and 

Silurian aquifers (layers 3 and 4) is 0.87 ft; the AVEH is 0.82 ft. 

The difference between the simulated and measured water 

levels is due to the model’s inability to represent the complex 

ground-water flow system.

Transient Calibration

Transient calibration of the ground-water flow model to 

hydrologic conditions measured from February 6, 1998, to 

March 16, 1998, was completed by comparing the change in 

simulated water level to the change in measured water level. 

Changes in river stage, recharge, and evapotranspiration with 

respect to time, were measured or estimated and included in the 

simulation. The changes reflect a “spring-thaw event,” a period 

of time that is best characterized as a condition that ranged from 

frozen soil and snow cover to snowmelt, soil thaw, and rain. 

Thirty-nine 1-day stress periods were used to simulate the variable pumping from the municipal wells that occurred during 

this time frame (table 5) and the change in Cedar River stage 

(table 6, fig. 11). The initial conditions for the transient model 

were established by a 50-day simulation using stresses associated with February 6, 1998, for which recharge was zero to simulate frozen soil conditions and an order of magnitude decrease 

in riverbed conductance to simulate siltation due to low streamflow in the Cedar River during the preceding winter months. 

The riverbed conductance was increased to the assumed steadystate levels after stress period 5 (February 10, 1998), which 

coincides with the beginning of the simulated increase in river 

stage and flow to represent scour of some of the riverbed siltation due to the increased streamflow. Recharge was increased 

and decreased during stress periods by using a multiplication 

factor applied to the steady-state recharge rate to account for 

periods of rain and snowmelt (fig. 12). Recharge during periods 

of no precipitation was assumed to be zero.

Some model parameters common to both the steady-state 

and transient simulations produced adequate results during the 

steady-state model calibration and were further refined during 

the transient-model calibration process. These adjustments 

improved both the steady-state and transient simulation and 

produced a better fit to the measured data. 
24 Simulation of Ground-Water Flow in the Cedar River Alluvial Aquifer Flow System, Cedar Rapids, Iowa

Table 5. Municipal pumpage rates used in the transient ground-water flow model calibration.

[Wells listed in table 2 that are not listed in this table had no simulated pumpage during the transient simulation; negative number indicates withdrawal;

ft3/s, cubic feet per second]

Stress 

period

Pumpage (ft3/s)

West well field (fig. 2), well number Seminole well field (fig. 2), well number

W11 W10 W9 W7 W4 W3 W2 S23 S19 S17 S15

1 -2.408 -2.248 -2.408 -2.248 -2.248 -2.248 -2.408 -2.248 0.000 -2.228 -2.228

2 -2.408 -2.248 -2.408 -2.248 -2.248 -2.248 -2.408 -2.248 0.000 -2.228 -2.228

3 -2.408 -2.248 -2.408 -2.248 -2.248 -2.248 -2.408 -2.248 0.000 -2.228 -2.228

4 -2.408 -2.248 -2.408 -2.248 -2.248 -2.248 -2.408 -2.248 0.000 -2.228 -2.228

5 -2.408 -2.248 -2.408 -2.248 -2.248 -2.248 -2.408 -2.248 0.000 -2.228 -2.228

6 -2.408 -2.248 -2.408 -2.248 -2.248 -2.248 -2.408 -2.248 0.000 -2.228 -2.228

7 -2.408 -2.248 -2.408 -2.248 -2.248 -2.248 -2.408 -2.248 0.000 -1.671 -2.228

8 -2.408 -2.248 -2.408 -2.248 -2.248 -2.248 -2.408 -2.248 0.000 -2.228 -2.228

9 -2.408 -2.248 -2.408 -2.248 -2.248 -2.248 -2.408 -2.248 0.000 -2.228 -2.228

10 -2.408 -2.248 -2.408 -2.248 -2.248 -2.248 -2.408 -2.248 0.000 -2.228 -2.228

11 -2.408 -2.248 -2.408 -2.248 -2.248 -2.248 -2.408 -2.248 0.000 -2.228 -2.228

12 -2.408 -2.248 -2.408 -2.248 -2.248 -2.248 -2.408 -2.248 0.000 -2.228 -2.228

13 -2.408 -2.248 -2.408 -2.248 -2.248 -2.248 -2.408 -2.248 0.000 -2.228 -2.228

14 -2.408 -2.248 -2.408 -2.248 -2.248 -2.248 -2.408 -2.248 0.000 -2.228 -1.114

15 -2.408 -2.248 -2.408 -2.248 -2.248 -2.248 -2.408 -2.248 0.000 -2.228 0.000

16 -2.408 -2.248 -2.408 -2.248 -2.248 -2.248 -2.408 -2.248 0.000 -2.228 0.000

17 -1.806 -2.248 -2.408 -2.248 -2.248 -2.248 -2.408 -2.248 0.000 -2.228 0.000

18 0.000 -2.248 -2.408 -2.248 -2.248 -2.248 -2.408 -2.248 0.000 -2.228 0.000

19 0.000 -2.248 -2.408 -2.248 -2.248 -2.248 -2.408 -2.248 -2.408 -2.228 0.000

20 0.000 -2.248 -2.408 -2.248 -2.248 -2.248 -2.408 -2.248 -1.873 -1.114 0.000

21 0.000 -2.248 -2.408 -2.248 -2.248 -2.248 -2.408 -2.248 -1.873 0.000 0.000

22 0.000 -2.248 -2.408 -2.248 -2.248 -2.248 -2.408 -2.248 -1.873 0.000 0.000

23 0.000 -2.248 -2.408 -2.248 -2.248 -2.248 -2.408 -2.248 -1.873 0.000 0.000

24 0.000 -2.248 -2.408 -2.248 -2.248 -2.248 -2.408 -2.248 -1.873 0.000 0.000

25 0.000 -2.248 -2.408 -2.248 -2.248 -2.248 0.000 -2.248 -1.873 0.000 0.000

26 0.000 -2.248 -2.408 -2.248 -2.248 -2.248 -2.408 -2.248 -1.873 0.000 0.000

27 0.000 -2.248 -2.408 -2.248 -1.124 -2.248 -2.408 -2.248 -1.873 0.000 0.000

28 0.000 -2.248 -2.408 -2.248 0.000 -2.248 -2.408 -2.248 -1.873 0.000 0.000

29 0.000 -2.248 -2.408 -2.248 0.000 -2.248 -2.408 -2.248 -1.873 0.000 -2.228

30 0.000 -2.248 -2.408 -2.248 0.000 -2.248 -2.408 -2.248 -1.873 0.000 -2.228

31 0.000 -2.248 -2.408 -2.248 0.000 -2.248 0.000 -2.248 -1.873 0.000 -2.228

32 0.000 -2.248 -2.408 -2.248 0.000 -2.248 0.000 -2.248 -1.873 0.000 -2.228

33 0.000 -2.248 -2.408 -2.248 0.000 -2.248 0.000 -2.248 -1.873 0.000 -2.228

34 0.000 -2.248 -2.408 -2.248 0.000 -2.248 0.000 -2.248 -1.873 0.000 -2.228

35 0.000 -2.248 -2.408 -2.248 0.000 -2.248 0.000 -2.248 -1.873 0.000 -2.228

36 0.000 -2.248 -2.408 -2.248 0.000 -2.248 0.000 -2.248 -1.873 0.000 -2.228

37 0.000 -2.248 -2.408 -2.248 0.000 -2.248 0.000 -2.248 -1.873 0.000 -2.228

38 0.000 -2.248 -2.408 -2.248 0.000 -2.248 0.000 -2.248 -1.873 0.000 -2.228

39 0.000 -2.248 -2.408 -2.248 0.000 -2.248 0.000 -2.248 -1.873 0.000 -2.228
Simulation of Ground-Water Flow 25

Table 5. Municipal pumpage rates used in the transient ground-water flow model calibration.—Continued

Stress

period

Pumpage (ft3/s)

Seminole well field (fig. 2), well number East well field (fig. 2), 

well number

S14 S13 S11 S9 S8 S7 S6 S5 S4 S2 E20 E18

1 -2.408 -2.408 0.000 -2.408 -2.408 -2.408 0.000 0.000 0.000 -2.408 0.000 -2.408

2 -2.248 -2.248 0.000 0.000 0.000 -2.228 0.000 0.000 0.000 -2.228 0.000 0.000

3 -2.248 -2.248 0.000 0.000 0.000 -2.228 0.000 0.000 0.000 -2.228 0.000 0.000

4 0.000 0.000 0.000 0.000 0.000 -2.228 0.000 0.000 0.000 -2.228 0.000 -0.562

5 -2.248 -2.248 0.000 0.000 0.000 -2.228 0.000 0.000 0.000 -1.671 0.000 -1.124

6 -2.248 -2.248 0.000 0.000 0.000 -1.114 0.000 0.000 0.000 -1.114 0.000 0.000

7 -2.248 -2.248 0.000 0.000 0.000 -2.228 0.000 0.000 0.000 -2.228 0.000 0.000

8 -2.248 -2.248 0.000 0.000 0.000 -2.228 0.000 0.000 0.000 -2.228 0.000 0.000

9 -2.248 -2.248 0.000 0.000 0.000 -2.228 0.000 0.000 0.000 -2.228 0.000 0.000

10 -2.248 -2.248 0.000 0.000 0.000 -2.228 0.000 0.000 0.000 -2.228 0.000 0.000

11 -2.248 -2.248 0.000 0.000 0.000 -2.228 0.000 0.000 0.000 0.000 0.000 -0.562

12 -2.248 -2.248 -2.408 0.000 0.000 -2.228 -2.408 0.000 0.000 -2.228 0.000 0.000

13 -2.248 -2.248 -1.686 0.000 0.000 -2.228 -1.686 0.000 0.000 -2.228 0.000 0.000

14 -1.124 -1.124 0.000 -0.937 -1.114 -2.228 0.000 -2.408 0.000 -2.228 0.000 -1.124

15 0.000 0.000 -2.248 0.000 0.000 -2.228 -2.248 -1.124 -2.408 -2.228 0.000 -1.124

16 0.000 0.000 -2.248 0.000 0.000 -2.228 -2.248 -2.248 -0.937 -2.228 0.000 0.000

17 0.000 0.000 -2.248 0.000 0.000 -2.228 -2.248 -2.248 -1.873 -2.228 0.000 0.000

18 0.000 0.000 -2.248 0.000 0.000 -2.228 -2.248 -2.248 -1.873 -2.228 -2.408 -1.124

19 0.000 0.000 -2.248 0.000 0.000 -2.228 -2.248 -2.248 0.000 -2.228 -1.124 -2.248

20 0.000 0.000 -2.248 0.000 0.000 -2.228 -2.248 -2.248 0.000 -2.228 0.000 -2.248

21 0.000 0.000 -2.248 0.000 0.000 -2.228 -2.248 -2.248 0.000 -2.228 0.000 -2.248

22 0.000 0.000 -2.248 0.000 0.000 -2.228 -2.248 -2.248 0.000 -2.228 0.000 -2.248

23 0.000 0.000 -2.248 0.000 0.000 -2.228 -2.248 -2.248 0.000 -2.228 0.000 -2.248

24 0.000 0.000 -2.248 0.000 0.000 -2.228 -2.248 -2.248 0.000 -2.228 0.000 -1.686

25 0.000 0.000 -2.248 0.000 0.000 -2.228 -2.248 -2.248 -0.937 -2.228 0.000 -1.686

26 0.000 0.000 -2.248 0.000 0.000 -2.228 -2.248 -2.248 -1.873 -2.228 -1.124 -0.562

27 -1.124 -1.124 -2.248 0.000 0.000 -2.228 -2.248 -2.248 -1.873 -2.228 -2.248 0.000

28 0.000 0.000 -2.248 0.000 0.000 -2.228 -2.248 -2.248 -1.873 -2.228 -2.248 0.000

29 -1.124 -1.124 -2.248 0.000 0.000 -2.228 -2.248 -2.248 -1.873 -2.228 -2.248 -1.686

30 0.000 0.000 -2.248 0.000 0.000 -2.228 -2.248 -2.248 -1.873 -2.228 -2.248 0.000

31 0.000 0.000 -2.248 0.000 0.000 -2.228 -2.248 -2.248 -1.873 0.000 -2.248 0.000

32 0.000 0.000 -2.248 0.000 0.000 -2.228 -2.248 -2.248 -1.873 0.000 0.000 -1.686

33 0.000 0.000 -2.248 0.000 0.000 -2.228 -2.248 -2.248 -1.873 0.000 0.000 0.000

34 -2.248 -2.248 -2.248 0.000 0.000 -2.228 -2.248 -2.248 -1.873 -2.228 0.000 0.000

35 -2.248 -2.248 -2.248 0.000 0.000 -2.228 -2.248 -2.248 -1.873 -2.228 0.000 0.000

36 -2.248 -2.248 -2.248 0.000 0.000 -2.228 -2.248 -2.248 -1.873 -2.228 0.000 0.000

37 -2.248 -2.248 0.000 0.000 0.000 -2.228 0.000 -2.248 -1.873 -2.228 0.000 0.000

38 -2.248 -2.248 0.000 0.000 0.000 -2.228 0.000 -2.248 -0.468 -2.228 0.000 0.000

39 -2.248 -2.248 -2.248 0.000 0.000 -2.228 -2.248 -1.686 0.000 -2.228 0.000 0.000
26 Simulation of Ground-Water Flow in the Cedar River Alluvial Aquifer Flow System, Cedar Rapids, Iowa

Table 5. Municipal pumpage rates used in the transient ground-water flow model calibration.—Continued

Stress

period

Pumpage (ft3/s)

East well field (fig. 2), well number

Collector wells (fig. 2),

well number

E17 E16 E14 E13 E10 E4 E3 E2 RANEY1 RANEY2

1 -2.408 -2.408 -2.408 -2.408 -2.408 -2.408 -2.408 -2.408 -5.581 -9.469

2 -1.124 0.000 -2.248 -2.248 0.000 -2.248 -2.565 0.000 -5.581 -9.469

3 -1.686 0.000 -2.248 -2.248 0.000 -2.248 -2.565 0.000 -5.581 -9.469

4 0.000 -2.248 -2.248 -2.248 0.000 -2.248 -2.565 0.000 -5.581 -9.469

5 -0.562 -2.248 -2.248 -2.248 0.000 -1.124 -2.565 -0.562 -5.581 -9.469

6 0.000 -2.248 -2.248 -2.248 0.000 -2.248 -2.565 0.000 -4.185 -7.106

7 0.000 -2.248 -2.248 -2.248 0.000 -2.248 -2.565 0.000 -5.581 -9.469

8 0.000 -2.248 -2.248 -2.248 0.000 -2.248 -2.565 0.000 -5.581 -9.469

9 0.000 -2.248 -2.248 -2.248 0.000 -2.248 -2.565 0.000 -5.581 -9.469

10 0.000 -2.248 -2.248 -2.248 0.000 -2.248 -2.565 0.000 -5.581 -9.469

11 -1.124 -2.248 -2.248 -2.248 0.000 -2.248 -2.565 -1.124 -5.581 -9.469

12 0.000 -1.124 -2.248 -2.248 0.000 -2.248 -2.565 -1.124 -5.581 -9.469

13 0.000 -1.124 -2.248 -2.248 0.000 -2.248 -2.565 -2.248 -5.581 -9.469

14 -1.124 -0.562 -2.248 -2.248 0.000 -2.248 -2.565 -2.248 -5.581 -9.469

15 -0.562 -0.562 -1.686 -1.686 0.000 -2.248 -2.565 -2.248 -5.581 -9.469

16 0.000 0.000 -1.686 -1.686 0.000 -2.248 -2.565 -2.248 -5.581 -9.469

17 0.000 -2.248 -2.248 -2.248 0.000 -2.248 -2.565 -2.248 -5.581 -9.469

18 -1.124 0.000 -2.248 -2.248 0.000 -2.248 -2.565 -2.248 -5.581 -9.469

19 -2.248 0.000 -2.248 -2.248 0.000 -1.124 -2.565 -2.248 -5.581 -9.469

20 -2.248 -2.248 -2.248 -2.248 0.000 0.000 -1.923 -1.686 -5.581 -9.469

21 -2.248 -2.248 -2.248 -2.248 0.000 0.000 0.000 0.000 -5.581 -9.469

22 -2.248 -2.248 -2.248 -2.248 0.000 0.000 0.000 -2.248 -5.581 -9.469

23 -2.248 -2.248 -2.248 -2.248 0.000 0.000 0.000 -2.248 -5.581 -9.469

24 -2.248 -2.248 -2.248 0.000 0.000 0.000 0.000 -1.686 -5.581 -9.469

25 -2.248 -2.248 -1.686 0.000 0.000 0.000 0.000 -2.248 -5.581 -9.469

26 -2.248 -2.248 0.000 0.000 -0.937 0.000 0.000 -2.248 -5.581 -9.469

27 -2.248 -2.248 -2.248 0.000 -0.937 0.000 0.000 -2.248 -5.581 -9.469

28 -2.248 -2.248 -2.248 0.000 0.000 0.000 -1.282 -2.248 -5.581 -9.469

29 -2.248 -2.248 -2.248 -0.562 0.000 0.000 -2.565 -2.248 -5.581 -9.469

30 -2.248 -2.248 -2.248 0.000 0.000 0.000 -2.565 -2.248 -5.581 -9.469

31 -2.248 -2.248 -2.248 0.000 0.000 -1.124 0.000 0.000 -5.581 -9.469

32 -2.248 -2.248 -1.124 0.000 0.000 0.000 -2.565 -2.248 -5.581 -9.469

33 -2.248 -2.248 -1.686 -1.686 0.000 0.000 -2.565 -2.248 -5.581 -9.469

34 -2.248 -2.248 -1.124 -1.124 -1.873 0.000 -2.565 -2.248 -5.581 -9.469

35 -2.248 -2.248 0.000 0.000 -1.873 0.000 -2.565 -2.248 -5.581 -9.469

36 -2.248 -2.248 0.000 0.000 -1.873 0.000 -2.565 -2.248 -5.581 -9.469

37 0.000 0.000 -1.124 -1.124 0.000 0.000 -2.565 -2.248 -5.581 -9.469

38 0.000 0.000 -2.248 -2.248 0.000 0.000 -2.565 -2.248 -5.581 -9.469

39 -2.248 -2.248 -1.124 -2.248 0.000 0.000 -2.565 -2.248 -5.581 -9.469
Simulation of Ground-Water Flow 27

Table 6. Cedar River stage during the transient ground-water simulation and incremental adjustment factor used in the transient river 

package.

[NAVD 88, North American Vertical Datum of 1988]

Stress

period

Date of

simulation

Cedar River at Cedar Rapids 

gage datum

(feet above NAVD 88)

Estimated stage 

above gagingstation datum

(feet)

Estimated stage

(feet above NAVD 88)

Change in Cedar River stage 

from stress period one

(feet)

1 02/06/98 700.47 3.66 704.13 0.00

2 02/07/98 700.47 3.66 704.13 0.00

3 02/08/98 700.47 3.66 704.13 0.00

4 02/09/98 700.47 3.66 704.13 0.00

5 02/10/98 700.47 3.68 704.15 0.02

6 02/11/98 700.47 3.81 704.28 0.15

7 02/12/98 700.47 4.00 704.47 0.34

8 02/13/98 700.47 4.11 704.58 0.45

9 02/14/98 700.47 3.97 704.44 0.31

10 02/15/98 700.47 3.88 704.35 0.22

11 02/16/98 700.47 3.85 704.32 0.19

12 02/17/98 700.47 4.00 704.47 0.34

13 02/18/98 700.47 4.45 704.92 0.79

14 02/19/98 700.47 4.67 705.14 1.01

15 02/20/98 700.47 4.96 705.43 1.30

16 02/21/98 700.47 5.26 705.73 1.60

17 02/22/98 700.47 5.44 705.91 1.78

18 02/23/98 700.47 5.48 705.95 1.82

19 02/24/98 700.47 5.40 705.87 1.74

20 02/25/98 700.47 5.27 705.74 1.61

21 02/26/98 700.47 5.24 705.71 1.58

22 02/27/98 700.47 5.42 705.89 1.76

23 02/28/98 700.47 5.55 706.02 1.89

24 03/01/98 700.47 5.52 705.99 1.86

25 03/02/98 700.47 5.44 705.91 1.78

26 03/03/98 700.47 5.36 705.83 1.70

27 03/04/98 700.47 5.28 705.75 1.62

28 03/05/98 700.47 5.22 705.69 1.56

29 03/06/98 700.47 5.14 705.61 1.48

30 03/07/98 700.47 5.06 705.53 1.40

31 03/08/98 700.47 5.05 705.52 1.39

32 03/09/98 700.47 4.95 705.42 1.29

33 03/10/98 700.47 4.74 705.21 1.08

34 03/11/98 700.47 4.56 705.03 0.90

35 03/12/98 700.47 4.42 704.89 0.76

36 03/13/98 700.47 4.43 704.90 0.77

37 03/14/98 700.47 4.44 704.91 0.78

38 03/15/98 700.47 4.49 704.96 0.83

39 03/16/98 700.47 4.54 705.01 0.88
28 Simulation of Ground-Water Flow in the Cedar River Alluvial Aquifer Flow System, Cedar Rapids, Iowa

Figure 12. Precipitation and snow cover at the Eastern Iowa Airport near Cedar Rapids, Iowa, and corresponding recharge multiplier 

for each transient model stress period.

0

1

2

3

4

5

6

7

8

2/62/72/82/9

2/102/112/122/132/142/152/162/172/18

2/19

2/202/212/222/232/242/252/262/272/28

3/13/23/33/43/53/63/73/83/9

3/103/113/123/133/143/153/16

DATE

PRECIPITATION OR SNOW COVER, IN INCHES

Precipitation, in inches of rainfall

Precipitation, in inches of snowfall

Snow cover, in inches

TOTAL PRECIPITATION FEBRUARY 1998

TOTAL PRECIPITATION MARCH 1998

AVERAGE MONTHLY PRECIPITATION

MARCH 1961-90

AVERAGE MONTHLY PRECIPITATION

MARCH 1961-90

0.000.000.000.000.002.56

0.210.00

0.00

0.00

0.00

1.39

0.000.000.000.000.00

1.070.750.006.305.551.280.750.21

0.750.530.000.11

0.00

9.82

0.21

0.000.00

0.00

0.00

0.000.000.00

RECHARGE RATE MULTIPLIER 

National Oceanic and Atmospheric Administration, 1999

The simulated transient water levels for cells near most (15 

of 23) of the observation wells (table 7) react to the changing 

stresses in the transient simulation similarly to measured water 

levels as illustrated by wells CRM11, CRM12, and CRM18 

(fig. 13). Differences between simulated water levels and 

measured water levels at some locations are possibly due to 

pumpage or other stresses not accounted for in the transient 

model. 

Sensitivity Analysis

A sensitivity analysis evaluates the response of the model 

to incremental changes in parameters to determine which 

parameters have the greatest effect on results. Model parameters were incrementally varied by at least one order of magnitude to test for sensitivity. The RMSE was used to quantify the 

effect of a parameter change on the steady-state model results.

Results of the sensitivity analysis for each change in a 

parameter is listed in table 8, which includes the effect of the 

parameter change on the resulting overall model RMSE and on 

the volumetric budget of the Cedar River. The model is most 

sensitive to tributary streambed (drain cell) conductance and 

horizontal hydraulic conductivity in layer 2. Substantial change 

in model fit was noted when the hydraulic conductivity in 

layer 5 is increased or decreased by an order of magnitude; 

however, only one observation well measures that change, and 

this may skew the actual significance of the parameter change 

on layer 5 results. The total amount of water moving into or out 

of the river is most sensitive to Cedar River riverbed conductance, horizontal hydraulic conductivity in layer 2, and 

recharge. 

Some parameters in the model, when adjusted more than 

two orders of magnitude, had little effect on the final solution. 

The model is insensitive to hydraulic conductivities of layers 3 

and 4, which is likely due to the minor extent of the geologic 

units (fig. 5) represented by these two layers near the observation wells. The model also is insensitive to changes in the 

general-head boundary conductance, which is likely due to the 

distance between the boundaries and the alluvium where water 

levels were measured. If improvement of the model is desired, 

additional data collection would be directed toward refining the 

most sensitive parameter(s).
Simulation of Ground-Water Flow 29

Table 7. Difference between measured and simulated water levels in selected wells within the study area, February 6, 1998, to 

March 16, 1998.

[Difference, in feet, between measured and simulated water level (measured minus simulated)]

Date Stress period CRM3 CRM4 CRM6 CRM7 CRM9 CRM11 CRM12 CRM15 CRM16

02/06/98 1 0.39 -5.08 8.54 -0.68 -0.81 -4.79 1.08 -5.27 -5.63

02/07/98 2 0.08 -5.57 8.38 -0.81 -0.93 -4.68 0.82 -6.24 -6.52

02/08/98 3 -0.81 -5.87 8.10 -0.95 -1.04 -4.64 0.42 -6.90 -7.17

02/09/98 4 -0.93 -6.08 7.90 -1.08 -1.06 -4.63 0.32 -7.45 -7.66

02/10/98 5 -1.07 -6.22 7.68 -1.30 -1.25 -4.71 0.23 -7.89 -7.92

02/11/98 6 -1.27 -6.37 7.80 -1.20 -1.07 -5.03 0.19 -8.43 -8.09

02/12/98 7 -1.43 -6.71 7.34 -1.33 -1.42 -5.16 0.20 -8.60 -8.27

02/13/98 8 -1.41 -6.92 7.24 -1.43 -1.42 -5.23 0.15 -8.74 -8.38

02/14/98 9 -0.94 -6.66 7.23 -1.47 -1.52 -5.29 0.12 -8.63 -8.67

02/15/98 10 -0.91 -7.40 7.17 -1.38 -1.41 -4.50 0.26 -8.93 -8.61

02/16/98 11 -1.29 -7.20 7.43 -1.29 -1.19 -3.54 0.45 -8.98 -8.53

02/17/98 12 -1.95 -7.57 7.66 -1.22 -0.49 -4.19 0.63 -9.03 -7.80

02/18/98 13 -2.03 -7.88 6.98 -1.68 -1.53 -4.32 0.70 -9.14 -7.79

02/19/98 14 -2.14 -8.17 6.52 -2.06 -2.05 -4.57 0.76 -9.40 -8.33

02/20/98 15 -3.47 -8.38 6.31 -2.15 -2.09 -4.96 0.80 -9.86 -8.27

02/21/98 16 -4.26 -8.18 6.38 -2.03 -2.17 -5.19 0.79 -10.14 -9.10

02/22/98 17 -4.27 -7.58 6.54 -2.00 -2.06 -5.25 0.79 -10.29 -8.36

02/23/98 18 -4.41 -6.44 6.81 -2.11 -2.10 -5.47 0.81 -10.40 -7.40

02/24/98 19 -4.20 -5.02 7.33 -2.08 -2.23 -5.56 0.72 -10.35 -7.09

02/25/98 20 -4.99 -4.54 7.31 -2.39 -2.33 -6.13 0.66 -10.44 -6.83

02/26/98 21 -5.36 -3.82 8.17 -2.09 -0.99 -6.41 0.47 -10.38 -6.72

02/27/98 22 -5.04 -3.09 8.42 -1.93 -0.99 -6.15 0.35 -10.24 -6.36

02/28/98 23 -4.65 -2.57 8.04 -2.17 -2.28 -5.86 0.38 -10.08 -5.79

03/01/98 24 -3.40 -1.89 8.14 -2.21 -2.41 -5.71 0.37 -9.79 -5.27

03/02/98 25 -4.21 -1.55 8.24 -2.19 -2.29 -5.65 0.35 -9.50 -4.90

03/03/98 26 -4.34 -1.34 8.43 -2.13 -2.30 -5.57 0.46 -9.18 -4.65

03/04/98 27 -4.07 -1.29 8.48 -2.17 -2.11 -5.64 0.59 -8.75 -4.82

03/05/98 28 -4.12 -0.51 8.46 -2.15 -1.94 -5.53 0.48 -8.07 -4.46

03/06/98 29 -4.02 -0.60 8.59 -2.06 -1.89 -5.37 0.35 -7.66 -4.45

03/07/98 30 -4.08 -1.19 8.74 -1.88 -1.89 -6.01 0.19 -7.45 -4.26

03/08/98 31 -4.63 -1.45 9.18 -1.67 -1.64 -6.79 -0.01 -7.41 -4.13

03/09/98 32 -4.19 -1.21 8.94 -1.85 -1.86 -6.84 -0.10 -7.07 -4.12

03/10/98 33 -3.26 -1.08 9.70 -1.64 -1.78 -6.67 -0.16 -6.67 -4.17

03/11/98 34 -2.49 -0.83 10.19 -0.99 -1.09 -6.21 0.00 -6.20 -4.02

03/12/98 35 -2.20 -0.37 10.41 -0.37 -0.48 -5.88 0.27 -6.00 -4.15

03/13/98 36 -1.34 -0.60 9.84 -0.18 -0.14 -5.54 0.36 -6.30 -4.15

03/14/98 37 -1.56 -0.63 9.77 -1.29 -1.19 -5.36 0.12 -6.32 -4.28

03/15/98 38 -1.77 -0.90 9.86 -1.39 -1.47 -5.60 -0.12 -6.43 -4.60

03/16/98 39 -1.78 -0.90 9.54 -1.50 -1.48 -5.74 -0.14 -6.38 -4.81

Maximum 0.39 -0.37 10.41 -0.18 -0.14 -3.54 1.08 -5.27 -4.02

Minimum -5.36 -8.38 6.31 -2.39 -2.41 -6.84 -0.16 -10.44 -9.10

Mean -2.76 -4.09 8.15 -1.60 -1.55 -5.39 0.39 -8.33 -6.32
30 Simulation of Ground-Water Flow in the Cedar River Alluvial Aquifer Flow System, Cedar Rapids, Iowa

Table 7. Difference between measured and simulated water levels in selected wells within the study area, February 6, 1998, to

March 16, 1998.—Continued

[Difference, in feet, between measured and simulated water level (measured minus simulated)]

Date Stress period CRM17 CRM18 CRM19 CRM22 CRM23 CRM24 CRM25 CRM27 CRM28

02/06/98 1 -5.21 -5.39 -4.32 0.08 -2.69 -2.96 -0.81 -0.84 -8.99

02/07/98 2 -6.21 -5.93 -4.70 -0.12 -3.00 -3.19 -0.71 -0.46 -9.69

02/08/98 3 -6.79 -6.24 -4.96 -0.29 -3.25 -3.40 -0.81 -0.54 -10.25

02/09/98 4 -7.28 -6.56 -5.32 -0.40 -3.43 -3.54 -0.93 -0.63 -10.76

02/10/98 5 -7.48 -6.77 -5.82 -0.55 -3.60 -3.70 -1.08 -0.78 -11.10

02/11/98 6 -8.02 -6.92 -5.82 -0.74 -3.79 -3.89 -1.31 -1.02 -11.20

02/12/98 7 -7.83 -7.01 -5.74 -0.89 -3.97 -4.05 -1.50 -1.19 -11.36

02/13/98 8 -7.90 -7.15 -6.06 -0.89 -4.04 -4.08 -1.56 -1.21 -11.45

02/14/98 9 -8.26 -7.03 -5.90 -0.85 -4.06 -4.06 -1.56 -0.78 -11.47

02/15/98 10 -8.20 -7.34 -6.19 -0.84 -4.06 -4.05 -1.42 -0.75 -11.49

02/16/98 11 -8.30 -7.24 -6.27 -0.74 -4.01 -3.98 -1.42 -1.19 -11.45

02/17/98 12 -7.50 -7.76 -6.54 -1.11 -4.16 -4.25 -1.36 -1.60 -10.33

02/18/98 13 -7.47 -7.78 -6.75 -1.29 -4.28 -4.41 -1.70 -1.61 -9.65

02/19/98 14 -7.70 -8.00 -7.07 -1.43 -4.34 -4.52 -1.68 -1.60 -10.20

02/20/98 15 -7.80 -8.10 -6.74 -2.08 -3.83 -3.39 -1.81 -2.53 -10.88

02/21/98 16 -8.58 -7.80 -5.62 -3.11 -3.49 -2.85 -1.97 -2.89 -12.26

02/22/98 17 -7.89 -7.17 -5.01 -2.85 -3.50 -2.99 -2.08 -2.64 -11.81

02/23/98 18 -7.05 -6.60 -3.50 -1.62 -2.37 -2.50 -2.17 -2.59 -11.05

02/24/98 19 -6.73 -5.94 -2.37 -1.52 -1.64 -2.14 -2.28 -2.42 -10.94

02/25/98 20 -6.78 -6.18 -1.86 -4.18 -2.53 -1.89 -2.52 -3.01 -10.91

02/26/98 21 -6.36 -6.22 -3.33 -10.91 -2.74 -2.94 -2.26 -3.51 -10.82

02/27/98 22 -6.10 -5.65 -3.88 -9.89 -2.65 -3.06 -2.37 -3.41 -10.65

02/28/98 23 -6.08 -4.93 -4.21 -4.34 -2.74 -2.11 -2.74 -3.06 -10.48

03/01/98 24 -5.37 -4.58 -3.85 -2.61 -2.46 -1.74 -2.53 -1.85 -10.19

03/02/98 25 -4.80 -4.38 -2.95 -2.88 -3.83 -1.27 -2.34 -2.66 -9.94

03/03/98 26 -4.64 -4.21 -2.48 -2.72 -3.65 -2.54 -2.22 -2.74 -9.79

03/04/98 27 -4.79 -4.27 -1.63 -2.39 -3.18 -2.39 -2.15 -2.37 -9.67

03/05/98 28 -4.83 -3.85 -0.18 -2.41 -3.18 -2.32 -2.02 -2.37 -9.58

03/06/98 29 -4.81 -3.92 -0.97 -2.27 -3.03 -2.12 -1.94 -2.22 -9.57

03/07/98 30 -4.37 -4.02 0.70 -2.35 -3.05 -1.89 -1.91 -2.23 -9.57

03/08/98 31 -4.51 -4.09 1.42 -5.20 -3.52 -1.80 -1.95 -2.79 -9.65

03/09/98 32 -3.83 -3.86 0.63 -2.45 -3.16 -2.46 -1.80 -2.38 -9.65

03/10/98 33 0.57 -3.59 0.05 -2.25 -2.96 -2.16 -1.74 -1.48 -9.78

03/11/98 34 -0.27 -3.50 1.03 -1.55 -2.41 -1.50 -1.37 -0.88 -9.17

03/12/98 35 -0.24 -3.32 1.77 -0.58 -1.66 -1.03 -1.17 -0.52 -9.26

03/13/98 36 -4.04 -3.72 2.62 0.55 0.06 -0.23 0.02 0.57 -9.20

03/14/98 37 -1.74 -3.77 3.52 -0.62 -0.07 0.47 0.52 0.40 -9.67

03/15/98 38 -0.99 -3.95 4.22 -0.59 0.12 -0.77 0.34 0.16 -9.96

03/16/98 39 -2.53 -4.08 4.82 -0.94 -0.28 -0.66 0.06 -0.05 -10.08

Maximum 0.57 -3.32 4.82 0.55 0.12 0.47 0.52 0.57 -8.99

Minimum -8.58 -8.10 -7.07 -10.91 -4.34 -4.52 -2.74 -3.51 -12.26

Mean -5.61 -5.61 -2.80 -2.10 -2.94 -2.62 -1.54 -1.63 -10.36
Simulation of Ground-Water Flow 31

Table 8. Sensitivity analysis results for each model parameter.

[ft3/s, cubic feet per second; --, no data]

Model parameter

Factor used

to change

parameter

Root mean

square error

(feet)

Total flow into 

alluvium from 

Cedar River

(ft3/s)

Total flow out

of alluvium to

Cedar River

(ft3/s)

Calibrated steady-state model -- 1.44 59.8 51.3

Recharge - infiltration of precipitation 0.10 1.51 62.0 51.2

10.00 1.94 42.4 99.7

Cedar River bed conductance 0.10 2.87 44.4 39.4

10.00 1.31 154.4 149.9

Tributary streambed conductance 0.10 2.20 54.0 48.5

10.00 2.26 57.9 33.3

General-head boundary conductance 0.10 1.43 61.7 36.9

10.00 1.46 58.2 65.8

Layer 1 Horizontal hydraulic conductivity 0.10 1.92 57.9 52.3

10.00 1.89 65.9 68.3

Vertical hydraulic conductivity 0.10 2.12 52.7 47.2

10.00 1.45 62.3 58.6

Layer 2 Horizontal hydraulic conductivity 0.10 3.02 33.7 34.0

10.00 2.90 54.5 102.7

Vertical hydraulic conductivity 0.10 2.23 54.8 45.1

10.00 1.43 61.2 52.9

Layer 3 Horizontal hydraulic conductivity 0.10 1.55 61.4 49.2

10.00 1.56 53.5 65.4

Vertical hydraulic conductivity 0.10 1.43 59.8 50.8

10.00 1.44 59.8 51.4

Layer 4 Horizontal hydraulic conductivity 0.10 1.42 60.3 50.2

10.00 1.77 57.4 57.4

Vertical hydraulic conductivity 0.10 1.43 60.0 50.0

10.00 1.44 59.6 52.2

Layer 5 Horizontal hydraulic conductivity 0.10 1.51 61.6 45.2

10.00 4.11 50.3 74.7

Vertical hydraulic conductivity 0.10 4.14 60.0 49.6

10.00 1.47 60.2 52.3
32 Simulation of Ground-Water Flow in the Cedar River Alluvial Aquifer Flow System, Cedar Rapids, Iowa

Figure 13. Simulated water levels in layer 2 compared to measured water levels in layer 2 for observation wells (A) CRM11, (B) CRM12, 

(C) CRM18, February 6, 1998, to March 16, 1998.

708

710

712

714

716

718

720

2/62/8

2/102/122/142/162/182/20

2/222/242/262/28

3/23/43/63/8

3/103/123/143/16

DATE

WATER LEVEL, IN FEET ABOVE NAVD 88

A

CRM11 Simulated

CRM11 Measured

712

714

716

718

720

722

724

B

CRM12 Simulated

CRM12 Measured

710

712

714

716

718

720

722

C CRM18 Simulated

CRM18 Measured
Simulation of Ground-Water Flow 33

Model Limitations

The ground-water flow model described in this report is an 

approximation of a complex ground-water flow system that can 

be used by water planners to help estimate the ground-water 

system’s response to variable stresses, whether anthropogenic 

or climatic. However, the model is limited in complexity with 

respect to the actual flow system and the following limitations 

should be noted:

1. The size of the model area is extensive and the number of 

model cells greatly exceeds the number of observation 

sites used for the calibration of the steady-state and transient models. The accuracy to which this model represents 

the area outside of the Cedar Rapids well fields is 

unknown due to the lack of data in those areas.

2. The model is a simplified version of a complex 

hydrogeologic system. Although, conceptually, the 

lithology throughout the Cedar River alluvial aquifer is 

heterogeneous, the aquifer was divided into zones of 

similar hydraulic conductivities to decrease computation 

times and increase the stability of the model. 

3. The steady-state simulation used to establish 

hydrogeologic properties of the study area assumed that 

inflow equaled outflow on December 21, 1998. If this 

assumption was not correct, then the change in storage 

would contribute to model error.

4. The transient model is calibrated to a very specific and 

short time interval that tests the conceptual model with 

limited climatic stresses. Uncertainty may be introduced 

in simulations of different climatic situations and 

durations. 

5. The transient data set is small compared to the number of 

model cells and the extent of the Cedar Rapids well 

fields. Some wells located in the same area have different 

comparison results, which could be due to unaccounted 

for changes in model parameters or stresses.

Steady-State Results and Hypothetical Pumping 

Scenarios

The steady-state model calculates a water level at each cell 

centroid and a ground-water flux across each cell face. The simulated potentiometric surface for the Quaternary deposits, 

including the Cedar River alluvial aquifer (model layer 2), is 

shown in figure 14, areas with no potentiometric contour lines 

are upland areas with dry cells in layer 2. Model results indicate 

that ground-water flow is predominately from the upland 

glacial deposits to the Cedar River alluvial aquifer and then 

discharged either to the Cedar River or to municipal pumpage. 

These results compare reasonably with the configuration of the 

potentiometric surface of the alluvial aquifer measured on 

December 21, 1998 (fig. 4). Beyond the part of the alluvial 

aquifer in the vicinity of the municipal wells, where measured 

water-level data are sparse, the model compares reasonably to 

the conceptual ground-water flow pattern. 

The movement of water in the model is quantified by gradients between adjacent cells and layers. Most of the water in 

the model moves towards layer 2, primarily the model layer representative of the Cedar River alluvial aquifer and the municipal 

pumpage. Simulated steady-state discharge of the ground-water 

flow system through the alluvial aquifer to the Cedar River is 

51.3 ft3

/s, whereas 59.8 ft3/s of Cedar River water flows into 

the alluvial aquifer (table 9). Thus, there are gaining and losing 

reaches of the Cedar River with a net loss of 8.5 ft3

/s. This loss 

of streamflow appears to be a reasonable simulation of the interaction between the Cedar River and Cedar River alluvial 

aquifer. 

The water budget for the calibrated steady-state model was 

used to evaluate the model and determine if the model results 

were consistent with the simplified conceptual model. The 

primary sources of inflow to the modeled area are infiltration 

from the Cedar River (53.0 percent) and regional flow across 

general-head boundaries (34.1 percent). The primary sources of 

outflow from the modeled area are discharge to the Cedar River 

(45.4 percent) and pumpage (44.8 percent) (table 9).

Several steady-state pumping scenarios were simulated 

using the calibrated steady-state model. All parameters were 

left unchanged from the steady-state model with the exception 

of pumpage. The first scenario reduced pumpage at all municipal wells to zero, producing results that could be assumed to be 

predevelopment conditions of the alluvial aquifer. In predevelopment conditions, most of the ground-water recharge would be 

from precipitation and most of the ground-water discharge 

would be to the Cedar River. In the northwestern portion of the 

model area just south of Palo where the Cedar River channel 

becomes braided and more complex, water moves into the 

Cedar River alluvial aquifer from the Cedar River (16 ft3/s, 

table 9). The presence of this losing reach in the northwestern 

part of the model area may be due to the simplified representation of this complex river-channel configuration in that portion 

of the model and may not be representative of steady-state conditions with no pumpage. However, losing reaches of the Cedar 

River have been noted in other areas of the Cedar River where 

water use is minor (Turco, 2002), indicating that the losing 

reach in this scenario may actually occur under predevelopment 

conditions. As expected, there is no river leakage into the Cedar 

River alluvial aquifer near the three Cedar Rapids well fields 

when pumpage is zero. 

Comparison of the predevelopment flow budget to the 

steady-state flow budget indicates that the steady-state pumpage of 50.6 ft3/s is primarily accounted for by an increase of 

43.8 ft3

/s in Cedar River inflow to the alluvial aquifer and 

6.5 ft3

/s of reduced outflow to the Cedar River (table 9). This 

water budget indicates that more than 99 percent of the water 

needed to supply the pumping is derived from the Cedar River.
34 Simulation of Ground-Water Flow in the Cedar River Alluvial Aquifer Flow System, Cedar Rapids, Iowa

Figure 14. Simulated potentiometric surface of model layer 2 near Cedar Rapids, Iowa, under steady-state conditions. Areas with 

missing contour lines are upland areas with dry cells.

River

Cedar

30

380

780

770

760

750

740

760

770 780

790

780

770

760

750

740

730

720

800

790

0

90

780

770

760

720

750

740

730

800

750

790

740

820

800

810

800

780

770

760

750

740

760

770 780

790

780

770

760

750

740

730

720

800

790

780

770

720

760

750

740

730

800

750

790

740

820

800

810

800

800

42o

04’

42o

41o

56’

91o48’ 91o44’ 91o40’

0 1 2 3 MILES

0 1 2 3 KILOMETERS

EXPLANATION

Potentiometric contour—Shows altitude at which water

 would have stood in tightly cased well. Contour interval

 10 feet. Vertical datum is NAVD 88

Cedar Rapids Cedar Rapids edar Rapids

Palo

Base from U.S. Geological Survey digital data, 1:100,000, 1995

Universal Transverse Mercator projection, Zone 15

North American Datum of 1983
Table 9. Water budgets for hypothetical steady-state pumping scenarios.[Inflow, water added to the ground-water system; outflow, water being removed from the ground-water system; pumpage, ground-water withdrawal by the City of Cedar Rapids, 

Budget component

Total pumpage at zero,

predevelopment condition

Total pumpage at assumed

steady-state condition

Total pumpage at a

steady-

Inflow

(ft3/s)

Percentage

of total

inflow

Outflow

(ft3/s)

Percentage

of total 

outflow

Inflow

(ft3/s)

Percentage

of total

inflow

Outflow

(ft3/s)

Percentage

of total 

outflow

Inflow

(ft3/s)

Percentag

of total

inflow

Recharge from 

infiltration of precipitation

14.6 21.1 0.0 0.0 14.6 12.9 0.0 0.0 14.6 9.0 

Flow between Cedar 

River and alluvium

16.0 23.2 57.8 83.7 59.8 53.0 51.3 45.4 109.7 67.3 

Flow from tributary 

streams to alluvium

.0 .0 10.8 15.7 .0 .0 10.6 9.4 .0 .0 

Pumpage .0 .0 .0 .0 .0 .0 50.6 44.8 .0 .0 General-head boundary 38.5 55.7 .4 .6 38.5 34.1 .4 .4 38.5 23.7 

Total 69.1 100.0 69.0 100.0 112.9 100.0 112.9 100.0 162.8 100.0 
36 Simulation of Ground-Water Flow in the Cedar River Alluvial Aquifer Flow System, Cedar Rapids, Iowa

The second scenario increased the overall pumpage of the 

calibrated steady-state model (101.1 ft3/s) by a factor of two. 

Initial simulations caused two wells in the East well field to go 

dry, mathematically eliminating their pumpage from the volumetric calculation and therefore reducing the total pumpage 

from the alluvial aquifer. To correct this situation and to ensure 

that the alluvium was stressed at about double the steady-state 

values during this scenario, a portion of the pumpage from those 

wells was assigned to a nearby well in the East well field. The 

simulated total infiltration from the Cedar River to the alluvium 

is 109.7 ft3

/s, including the inflow north of the well fields near 

Palo. For the approximately 100 years of record for the Cedar 

River at Cedar Rapids gaging station, streamflow has exceeded 

680 ft3

/s 90 percent of the time. The amount of induced infiltration is about 16 percent of this low flow. More than 99.5 percent 

of the pumpage is derived from water infiltrating from the 

Cedar River. There was little change (0.7 ft3/s) between the 

steady-state scenario and the nearly doubled steady-state 

scenario in the amount of water discharged from the alluvial 

aquifer to the river indicating that the gaining reaches of the 

river may not be affected much by the additional pumpage. 

Model results show that the Cedar River is in good hydraulic connection with the underlying alluvium and that the effects 

of the backwater siltation upstream from the low-head dam are 

small. With the high degree of connection with the Cedar River 

and the proximity of the municipal wells to the Cedar River, it 

seems reasonable that as long as there is sufficient flow in the 

Cedar River, ground-water availability in the Cedar Rapids area 

will not be significantly affected.

Transient Results and Hypothetical Pumping 

Scenarios

The transient pumping scenarios were developed to evaluate the timing of changes in water levels and ground-water flow 

due to changes in pumping. During the transient pumpage 

scenarios, all hydrogeologic parameters were left unchanged 

from the calibrated steady-state model. The stage of the Cedar 

River, the rate of recharge from infiltration of precipitation, and 

the rate of evapotranspiration also were held constant at steadystate values for each stress period. The only parameter varied 

was pumpage. The simulation consisted of 31 stress periods. 

Each of the first 30 stress periods are 1 day in length. Stress 

period 31 is 30 days long. Initial pumpage from all wells was 

zero, and incrementally increased every stress period until the 

full pumpage was reached at stress period 31 (fig. 15). This 

pumpage was then held constant for the remainder of the simulation. The final pumpage amount was larger than the amount 

for the steady-state scenarios because all wells were pumping 

rather than selected wells.

Figure 15. Pumpage and river inflow for transient model scenarios.

0

10

20

30

40

50

60

70

80

90

100

110

120

130

140

150

160

170

180

190

200

0 5 10 15 20 25 30 35 40 45 50 55 60

DAYS

PUMPAGE AND RIVER INFLOW, IN CUBIC FEET PER SECOND

River inflow 2x pumpage

Total 2x pumpage

River inflow 1x pumpage

Total 1x pumpage
Summary 37

The first transient scenario had a final pumpage rate of 

about 93.4 ft3

/s and shows that water begins to enter the alluvial 

aquifer from the Cedar River in less than 1 day after pumping 

begins. Induced recharge from the river continues to increase 

until, after about 15 days, the change in pumpage is about the 

same as the change in inflow from the Cedar River. Induced 

recharge continues to increase at a rate similar to the rate of 

pumpage increase until pumpage levels off. At that point, the 

induced recharge increases at a much slower rate. 

The second transient scenario involved increasing pumpage to about twice the rate of the first transient scenario, 

186.9 ft3/s. The rate in inflow from the Cedar River is about the 

same as the rate of pumpage after about 12 days during this 

scenario. The time it takes before an initial change in inflow 

from the Cedar River remains less than 1 day (fig. 15). 

Assuming that the induced recharge will meet 99 percent 

of the pumpage demand at equilibrium and that the rate of 

induced recharge will continue to decrease at a constant rate 

until equilibrium is reached, both transient simulations indicate 

that nearly 150 days will be needed to reach equilibrium 

between pumpage and river inflow.

Summary

The Cedar River alluvial aquifer is the primary source of 

municipal water in the Cedar Rapids, Iowa, area. Since 1992, 

the U.S. Geological Survey (USGS), in cooperation with the 

City of Cedar Rapids, has investigated the hydrogeology and 

water quality of the Cedar River alluvial aquifer. Since 1999, 

efforts have been underway to refine the analysis of groundwater/surface-water interactions reported in earlier efforts to 

focus specifically on the Cedar Rapids well field area.

The study area is located in east-central Iowa and encompasses an area of about 45 mi2 from Palo, Iowa, southeast to 

Cedar Rapids, surrounding the Cedar River alluvial aquifer. 

The area consists of a relatively flat alluvial valley bounded by 

upland areas. The Cedar River flows through the alluvial valley 

in the central portion of the study area, predominately from the 

northwest to the southeast. Alluvial deposits of aquifer material 

occur primarily as sand and gravel on the inside of river channel 

bends. Three Cedar Rapids municipal well fields (Seminole, 

West, and East) are located primarily north and east of the 

Cedar River. Two radial collector wells are located across from 

the Seminole well field, west of the Cedar River. Land use in 

much of the northwestern part of the study area is agricultural. 

Annual precipitation in the study area averages about 

36.39 in/yr.

Ground-water and surface-water data were collected 

during the study to better define the hydrogeology of the Cedar 

River alluvial aquifer and Devonian and Silurian aquifers, and 

to assist in construction of the ground-water flow model. 

Measured ground-water levels were used to evaluate the local 

flow directions in the study area, to evaluate the seasonal variation in horizontal and vertical ground-water flow, to aid in the 

development and validation of the conceptual ground-water 

flow system, and to aid in the calibration of steady-state and 

transient simulations. Streamflow and river-stage data have 

been collected periodically from 1902 to 2003 on the Cedar 

River in the study area as part of the USGS streamflowobservation network in Iowa. 

Unconsolidated geologic deposits and shallow bedrock 

units are in direct hydraulic connection in various combinations 

throughout the study area. The Cedar River alluvial aquifer is 

composed of sand, gravel, and minor amounts of silt and clay. 

The thickness of the alluvial aquifer decreases as distance from 

the Cedar River increases; the thinnest deposits are adjacent to 

the valley walls. Tributary stream alluvial aquifers and localized deposits of loess and eolian sand overlie the glacial till in 

the study area. A buried-channel aquifer is located along the 

northwestern border of the model area. The unconsolidated 

material in the upland areas bordering the alluvial aquifers in 

the study area consists predominately of glacial till. The Devonian aquifer is the uppermost bedrock in most of the study area 

outside the river valley and consists of fractured and unfractured limestone and dolomite. The Otis and Bertram Formations 

of Devonian age, composed predominately of limestone, dolomite, and a basal shale, form a local confining unit that restricts 

the flow of water between the Devonian and the underlying 

Silurian bedrock. The Silurian aquifer consists primarily of 

dolomite. In the Cedar River alluvial valley, the Devonian bedrock units, including the Otis and Bertram Formations, have 

been completely eroded leaving the Silurian bedrock as the 

uppermost bedrock unit. The Maquoketa Shale (Formation) of 

Ordovician age underlies the Silurian bedrock and is a regional 

confining unit. 

The ground-water flow system in the study area consists of 

two main components, the unconsolidated Quaternary deposits 

and the underlying bedrock that has a variable fracture density. 

In the absence of anthropogenic stresses on the Cedar River 

alluvial aquifer, ground-water flow is typically towards the 

Cedar River and down the Cedar River valley. Ground-water 

flow in the Devonian and Silurian aquifers is a regional flow 

system. Recharge to the bedrock aquifers occurs regionally 

where the bedrock is exposed at land surface or through vertical 

flow from overlying Quaternary deposits. 

Ground-water flow was simulated for the Cedar River 

alluvial aquifer and the Devonian and Silurian aquifers using 

the USGS’s three-dimensional finite-difference ground-water 

flow model MODFLOW. The flow model was constructed to 

simulate steady-state conditions and transient conditions. A 

transient simulation was performed to evaluate the effect of 

hypothetical pumping scenarios on the timing of water infiltrating the alluvial aquifer from the Cedar River. The model was 

discretized into 223 rows and 354 columns of cells. Cell sizes 

range from about 50 ft on a side near the Cedar River and the 

Cedar Rapids municipal wells to 1,500 ft on a side near the 

model boundaries and farthest away from the Cedar Rapids 

municipal well fields. The model grid covers approximately 

45 mi2

 and simulates ground-water flow in five layers, which 

include all hydrogeologic units. 
38 Simulation of Ground-Water Flow in the Cedar River Alluvial Aquifer Flow System, Cedar Rapids, Iowa

The ground-water flow model was calibrated by adjusting 

the value of model input parameters so that the resulting model 

output matched measured water levels and other hydrologic 

observations with a reasonable level of accuracy. Presumed 

steady-state water-level data were obtained during a synoptic 

water-level measurement on December 21, 1998. The root 

mean square error for the calibrated steady-state model is 

1.44 ft; the average model error is -0.26 ft. Transient calibration 

of the ground-water flow model to hydrologic conditions 

measured from February 6, 1998, to March 16, 1998, was completed by comparing the change in simulated water levels to the 

change in nearby measured water levels. The calibrated transient water levels near most of the observation wells responded 

similarly to measured water levels and the transient simulation 

compares reasonably with the conceptual flow model. 

The sensitivity of the model to incremental changes in 

parameter values and the limitations of this model are important 

considerations. The model is most sensitive to drain cell tributary streambed conductance and horizontal hydraulic conductivity in layer 2. The model is limited in complexity with respect 

to the actual system and the total number of observations available for calibration compared to the number of model cells is 

very small, which substantially contributes to the uncertainty of 

this model. 

Steady-state model water levels indicate that ground-water 

flow is predominately from the upland deposits to the Cedar 

River alluvial aquifer and then is discharged either to the Cedar 

River or to municipal pumpage. Most of the water moving in the 

ground-water flow model moves towards the Cedar River alluvial aquifer. The primary sources of inflow to the modeled area 

are infiltration from the Cedar River (53.0 percent) and regional 

flow across general-head boundaries (34.1 percent). The 

primary sources of outflow from the modeled area are discharge 

to the Cedar River (45.4 percent) and pumpage (44.8 percent). 

The current steady-state pumpage has increased the rate of 

inflow from the Cedar River to the alluvial aquifer by 43.8 ft3/s 

and reduced the rate of outflow from the alluvial aquifer to the 

Cedar River by 6.5 ft3/s over pre-development conditions. 

More than 99 percent of the water discharging from municipal 

wells infiltrates from the Cedar River. Results from steady-state 

pumpage scenarios indicate that the Cedar River alluvium can 

sustain double the steady-state pumpage with minimal effect on 

ground-water availability provided sufficient flow is available 

in the Cedar River to provide recharge to the aquifer.

Transient hypothetical pumpage scenarios were used to 

show the effect of changes in pumpage on the timing of infiltration of water from the Cedar River. Transient scenarios showed 

that as pumpage is increased from zero, river inflow begins to 

increase in less than 1 day. As pumpage from the Cedar Rapids 

well fields increases, infiltration of water into the alluvial 

aquifer from the Cedar River increases, and nearly 150 days 

may be needed for river infiltration to equilibrate with municipal pumpage.

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Prepared by the Iowa District office:

U.S. Geological Survey, WRD

Room 269, Federal Building

P.O. Box 1230

400 South Clinton Street

Iowa City, IA 52244

Text layout by Ella M. Decker, USGS, Huron, South Dakota.

Graphics layout by Connie J. Ross, USGS, Huron, South Dakota.

Information regarding the water resources in Iowa is available at URL

 http://ia.water.usgs.gov/

This publication is available online at URL

 http://pubs.water.usgs.gov/sir20045130
Printed on recycled paper

Turco and Buchmiller—Simulation of Ground-Water Flow in the Cedar River Alluvial Aquifer Flow System, Cedar Rapids, Iowa—SIR 2004-5130