Prepared in cooperation with Jefferson County and the Washington State Department of Ecology

Transient Calibration of a Groundwater-Flow Model of 

Chimacum Creek Basin and Vicinity, Jefferson County, 

Washington—A Supplement to Scientific Investigations 

Report 2013-5160

U.S. Department of the Interior

U.S. Geological Survey

Open-File Report 2013–1258

Transient Calibration of a Groundwater-Flow Model of 

Chimacum Creek Basin and Vicinity, Jefferson 

County, Washington—A Supplement to Scientific 

Investigations Report 2013-5160

By Joseph L. Jones and Kenneth H. Johnson 

 

Prepared in cooperation with Jefferson County and the Washington State Department of Ecology 

Open-File Report 2013–1258

U.S. Department of the Interior

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

SALLY JEWELL, Secretary

U.S. Geological Survey

Suzette M. Kimball, Acting Director

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

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Suggested citation:

Jones, J.L., and Johnson, K.H., 2013, Transient calibration of a groundwater-flow model of Chimacum 

Creek Basin and vicinity, Jefferson County, Washington—A supplement to Scientific Investigations 

Report 2013-5160: U.S. Geological Survey Open-File Report 2013-1258, 44 p., 

KWWSG[GRLRUJRIU

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

endorsement by the U.S. Government.

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

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

Contents

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

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

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

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

Groundwater-Flow System............................................................................................................................ 5

Numerical Simulation of the Groundwater-Flow System................................................................................ 8

Transient Calibration................................................................................................................................ 13

Possible Causes for Poor Calibration....................................................................................................... 41

Recommendations for Further Study ....................................................................................................... 42

Summary ..................................................................................................................................................... 42

References Cited......................................................................................................................................... 43

Figures

Figure 1. Map showing locations of surface-water measurements and wells used for calibration, 

Chimacum Creek Basin and vicinity, Jefferson County, Washington............................................................. 4

Figure 2. Graph showing historical groundwater use, Probable Future Use, steady-state Full 

Beneficial Use and total groundwater use for the Jefferson County Public Utility District #1, 

Chimacum Creek Basin and vicinity, Jefferson County, Washington, water years 1995–2030 ..................... 6

Figure 3. Maps showing areal distribution of storage coefficient values, with shading indicating 

where the storage coefficient is specified as confined, and locations of storage coefficient calibration 

pilot points for all model layers, Chimacum Creek Basin and vicinity, Jefferson County, Washington......... 17

Figure 4. Graph showing simulated and measured groundwater-level altitudes for the calibrated 

model for transient conditions, Chimacum Creek Basin and vicinity, Jefferson County, Washington.......... 23

Figure 5. Hydrographs of simulated and measured groundwater-level altitudes for the calibrated 

model for transient conditions, Chimacum Creek Basin and vicinity, Jefferson County, Washington.......... 26

Figure 6. Graph showing simulated and measured streamflow from groundwater discharge for the 

calibrated model for transient conditions, Chimacum Creek Basin and vicinity, Jefferson County, 

Washington.................................................................................................................................................. 37

Figure 7. Hydrographs of simulated and measured streamflow from groundwater discharge for the 

calibrated model for transient conditions, Chimacum Creek Basin and vicinity, Jefferson County, 

Washington.................................................................................................................................................. 38

Tables

Table 1. Water use by residents within the Jefferson County Public Utility District #1 (public-supply use), 

and by residents and agriculture outside the public-supply area (self-supplied use); and the resultant 

recharge of groundwater by return flow from each class of user, during each year of the recorded period 

1994–2009, Chimacum Creek basin and vicinity, Jefferson County, Washington ......................................... 7

Table 2. Wells used in calibration, Chimacum Creek and vicinity, Jefferson County, Washington............... 9

Table 3. Flow measurement locations used for calibration, Chimacum Creek and vicinity, Jefferson 

County, Washington .................................................................................................................................... 11

Table 4. Final values for calibration parameters.......................................................................................... 15

Table 5. Calibration statistics for the transient calibration by hydrogeologic unit and baseflow, 

Chimacum Creek and vicinity, Jefferson County, Washington..................................................................... 24
iv

Conversion Factors and Datums

Conversion Factors

Multiply By To obtain

Length

inch (in.) 2.54 centimeter (cm)

foot (ft) 0.3048 meter (m)

mile (mi) 1.609 kilometer (km)

Area

acre 0.4047 hectare (ha)

square mile (mi2) 259.0 hectare (ha)

Flow rate

acre-foot per year (acre-ft/yr) 1,233 cubic meter per year (m3/yr)

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

cubic foot per second (ft3/s) 0.02832 cubic meter per second (m3/s)

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

Transmissivity*

foot squared per day (ft2/d) 0.09290 meter squared per day (m2/d) 

*Transmissivity: The standard unit for transmissivity is cubic foot per day per square foot times foot of aquifer 

thickness [(ft3

/d)/ft2]ft. In this report, the mathematically reduced form, foot squared per day (ft2/d), is used for 

convenience.

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

°C=(°F-32)/1.8.

Datums

Vertical coordinate information is referenced to the North American Vertical Datum of 1988 (NAVD 88).

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

 

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

Well-Numbering System

Wells in Washington State are assigned a local well number that identifies each well based on its location within a 

township (T), range (R), section, and 40-acre tract. For example, well 29N/01W-35J01 refers to township (T. 29 N) and 

the range (R. 01 W) north of the Willamette Base Line and west of the Willamette Meridian. The first number 

following the hyphen indicates the section (35) within the township, and the letter (J) following the section number 

indicates the 40-acre subdivision of the section. The final two-digit number (01) uniquely distinguishes individual 

wells in the same 40-acre tract.
vi

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1 

Transient Calibration of a Groundwater-Flow Model of 

Chimacum Creek Basin and Vicinity, Jefferson 

County, Washington—A Supplement to Scientific 

Investigations Report 2013-5160

By Joseph L. Jones and Kenneth H. Johnson 

Abstract

A steady-state groundwater-flow model described in Scientific Investigations Report 

2013-5160, ”Numerical Simulation of the Groundwater-Flow System in Chimacum Creek Basin 

and Vicinity, Jefferson County, Washington” was developed to evaluate potential future impacts 

of growth and of water-management strategies on water resources in the Chimacum Creek Basin.

This supplement to that report describes the unsuccessful attempt to perform a calibration to 

transient conditions on the model. The modeled area is about 64 square miles on the Olympic 

Peninsula in northeastern Jefferson County, Washington. The geologic setting for the model area

is that of unconsolidated deposits of glacial and interglacial origin typical of the Puget Sound 

Lowlands. The hydrogeologic units representing aquifers are Upper Aquifer (UA, roughly 

corresponding to recessional outwash) and Lower Aquifer (LA, roughly corresponding to 

advance outwash). Recharge from precipitation is the dominant source of water to the aquifer 

system; discharge is primarily to marine waters below sea level and to Chimacum Creek and its 

tributaries.

The model is comprised of a grid of 245 columns and 313 rows; cells are a uniform 200 

feet per side. There are six model layers, each representing one hydrogeologic unit: (1) Upper 

Confining unit (UC); (2) Upper Aquifer unit (UA); (3) Middle Confining unit (MC); (4) Lower 

Aquifer unit (LA); (5) Lower Confining unit (LC); and (6) Bedrock unit (OE). The transient 

simulation period (October 1994–September 2009) was divided into 180 monthly stress periods 

to represent temporal variations in recharge, discharge, and storage.

An attempt to calibrate the model to transient conditions was unsuccessful due to 

instabilities stemming from oscillations in groundwater discharge to and recharge from 

streamflow in Chimacum Creek. The model as calibrated to transient conditions has mean 

residuals and standard errors of 0.06 ft ±0.45 feet for groundwater levels and 0.48 ± 0.06 cubic 

feet per second for flows. Although the expected seasonal trends were observed in model results, 

the typical observed annual variation of groundwater levels of about 2 feet was not. Streamflow 

at the most downstream observation point was about three times larger than simulated

streamflow. Because the transient version of the model proved inherently unstable, it was not 

used to simulate forecast conditions for alternate hydrologic or anthropogenic changes.

Adaptation of alternate stream simulation packages, such as RIV, or newer versions of 

MODFLOW, such as MODFLOW-NWT, could possibly assist with achieving calibration to 

transient conditions. 
2 

Introduction

A groundwater-flow model, described in Scientific Investigations Report 2013-5160, 

“Numerical Simulation of the Groundwater-Flow System in Chimacum Creek Basin and 

Vicinity, Jefferson County, Washington,” was developed in cooperation with Jefferson County 

and the Washington State Department of Ecology, to assess the potential effects of future 

population and water-use changes in the Chimacum Creek Basin and vicinity. The model was 

developed and calibrated for steady-state conditions to evaluate forecast population changes, full 

beneficial use of the Jefferson County Public Utility District #1 water rights, and conversion of 

septic systems to sanitary sewer system within the Urban Growth Area. The model also was used 

to evaluate the effects of groundwater withdrawals used for agriculture with respect to magnitude 

and depth of withdrawals. Particle tracking was used with the model to gain understanding of the 

locations of groundwater recharge with respect to the ultimate location of groundwater 

discharge. An analysis of model mass balances from many simulations with a single pumping 

well in different locations provided a map of the areal variation in response coefficients for the 

well, indicating the fraction of water being pumped by the well that resulted in lowered 

streamflow in Chimacum Creek. 

A transient calibration of the groundwater-flow model was attempted as well, in order to 

assess the temporal aspects of the aquifer response to the changes in population and water use 

that were studied with the steady-state application of the model. The calibration was achieved 

only by allowing the solution of the numerical simulation to halt before satisfactory convergence 

of the products of the governing equations was attained. As such, the calibration of a transient 

version of the model was deemed inappropriate for use in assessing the temporal aspects of 

changes in stresses to the aquifer system. 

Documentation of the attempt to calibrate a transient version of the steady-state model, 

however, was considered important, although not appropriate for inclusion in a report on the 

steady-state results. The range of variables considered, the magnitude of the differences between 

target calibration and simulated values, and possible approaches to achieve calibration that were 

not attempted could help future research efforts achieve success. This report is a supplement to 

Jones and others (2013) and presents the results of an attempt to calibrate a transient version of 

the Chimacum Creek groundwater-flow model. 

Purpose and Scope

The purpose of this report is to present the results of an attempt to calibrate a transient 

version of the steady-state model calibrated for and reported on by Jones and others (2013). It 

summarizes parts of the construction and calibration of the steady-state model that are relevant to 

the transient calibration. This report references figures and tables included in Jones and others 

(2013) that are not reproduced here. 
3 

Description of Study Area

The model covers an area of about 64 mi2 on the Olympic Peninsula in northeastern 

Jefferson County, Washington (fig. 1). The Chimacum Creek Basin drains an area of about 53 

mi2 and consists of Chimacum Creek and its tributary East Fork Chimacum Creek. These creeks 

converge near the town of Chimacum and discharge to Port Townsend Bay near the town of 

Irondale. The topography of the study area consists of narrow, regularly spaced parallel ridges 

and grooves that are characteristic of fluted glaciated surfaces; they are oriented in a north-south 

direction (Ritter, 1978). This surface has been incised locally by fluvial and postglacial erosion, 

producing steep sides and hummocky bottoms for the valley. Thick accumulations of peat occur 

along the axis of East Fork Chimacum Creek and provide rich, agriculturally productive soils. 

The study area is underlain by a north-thickening sequence of unconsolidated glacial and 

interglacial deposits. Sedimentary and igneous bedrock units underlie the unconsolidated 

deposits and crop out along the margins and the western interior of the study area. 

The study area has a temperate marine climate with warm, dry summers, and cool, wet 

winters. Chimacum Creek Basin lies within the rain shadow of the Olympic Mountains, and the 

annual average precipitation during 1981–2010 at the community of Center (fig. 1) was 28.78 

in/yr (National Oceanic and Atmospheric Administration, 2007). In 1996, the population of the 

Chimacum Creek Basin was 5,675 people, and is projected to increase by almost 30 percent by 

2016 (Parametrix and others, 2000). Population density in the basin is highest near the mouth of 

Chimacum Creek, in the general area of Irondale, Port Hadlock, and Chimacum (fig. 1). 
4 

Figure 1. Map showing locations of surface-water measurements and wells used for calibration, 

Chimacum Creek Basin and vicinity, Jefferson County, Washington.
5 

Groundwater-Flow System

The geologic setting for Chimacum Creek Basin and the adjacent lands to the west, 

bordering Discovery Bay, and to the east, bordering Port Townsend Bay and Oak Bay, are 

typical of the Puget Sound Lowlands; unconsolidated deposits of glacial and interglacial origin 

are present throughout the study area. A typical glacial sequence progresses from advance 

outwash, to till, to recessional outwash. Fluvial, lacustrine, bog, and marsh depositional 

environments were common during interglacial periods. The modern-day drainage pattern of 

Chimacum Creek is mostly determined by pre-existing drainage pathways established by Vashon 

recessional outwash channels.

As described in Jones and others (2011) and Jones and others (2013), aquifers consist 

primarily of coarse-grained glacial outwash, but they also may include coarse-grained sediments 

within glacial till and coarse-grained interglacial deposits. The hydrogeologic units representing 

aquifers are the Upper Aquifer unit (UA, model layer 2) and the Lower Aquifer unit (LA, model 

layer 4). The hydrogeologic units roughly correspond with geologic units recessional outwash 

(UA) and advance outwash (LA) of the Vashon glacial deposits. The Lower Confining unit (LC, 

model layer 5) is a productive aquifer in some places. In other places, hundreds of feet of clay 

make LC a confining unit. Because most wells are finished in UA and LA, there were 

insufficient data to credibly subdivide the LC interglacial deposits (and possibly deposits from 

pre-Vashon glacial epochs) into distinct geologic or hydrogeologic units. Confining units consist 

primarily of fine-grained glacial outwash, unsorted and compacted glacial till, glaciolacustrine 

deposits, and fine-grained interglacial deposits. The hydrogeologic units representing confining 

layers are the Upper Confining unit (UC, model layer 1) and the Middle Confining unit (MC, 

model layer 3). The Lower Confining (LC, model layer 5) is not distinctly a confining unit. UC 

roughly corresponds with geologic unit Quaternary alluvial, and MC roughly corresponds with 

Vashon till. Unconsolidated aquifer and confining units are underlain by low-permeability 

Eocene to Oligocene sedimentary and igneous bedrock (hydrogeologic unit Bedrock, OE, model 

layer 6). Jones and others (2013, figs. 1 and 4, table 1) are useful references for the orientation, 

extent, and composition of the aquifer and confining hydrogeologic units. 

Recharge from precipitation is the dominant source of water to the aquifer system. Return 

flow (recharge resulting from water use) from irrigation and septic systems contribute small 

amounts of recharge. Discharge is primarily to marine waters below sea level and to Chimacum 

Creek and its tributaries. Springs, seeps, and wells for public supply, domestic supply, and 

agriculture comprise the balance of groundwater discharge. Historical and projected publicsupply use of groundwater are shown in figure 2 and table 1. Jones and others (2013, fig. 3) 

shows the location and magnitude of recharge from precipitation; Jones and others (2013, table 

3) provides estimates of the major components of the groundwater budget. 
6 

Figure 2. Graph showing historical groundwater use, Probable Future Use, steady-state Full Beneficial 

Use and total groundwater use for the Jefferson County Public Utility District #1, Chimacum Creek Basin 

and vicinity, Jefferson County, Washington, water years 1995–2030.
7 

Table 1. Water use by residents within the Jefferson County Public Utility District #1 (public-supply use), 

and by residents and agriculture outside the public-supply area (self-supplied use); and the resultant 

recharge of groundwater by return flow from each class of user, during each year of the recorded period 

1994–2009, Chimacum Creek Basin and vicinity, Jefferson County, Washington. 

Water 

year

Source of usage or return flows, in acre-feet per year

PUD

Kala 

Point

Selfsupplied Irrigation

Precipitation 

Recharge

Public 

water 

return

(Probable 

Use) 

Agriculture 

return

Selfsupplied 

return

Probable 

Use

Full 

Beneficial 

Use

1995 622 1,406 172 179 327 18,261 567 76 121

1996 622 1,406 175 182 327 18,391 569 76 123

1997 501 1,406 176 183 327 19,476 487 76 124

1998 601 1,406 179 186 327 20,323 550 76 126

1999 597 1,406 181 189 327 23,108 566 76 128

2000 570 1,406 184 191 327 13,332 532 76 129

2001 599 1,406 189 197 327 13,055 559 76 133

2002 637 1,406 193 200 327 12,084 583 76 135

2003 695 1,406 195 203 327 13,297 623 76 137

2004 695 1,406 198 205 327 13,015 630 76 139

2005 665 1,406 201 209 327 13,727 608 76 141

2006 691 1,406 206 214 327 19,283 627 76 145

2007 688 1,406 208 216 327 13,956 631 76 146

2008 688 1,406 210 218 327 10,717 634 76 147

2009 751 1,406 211 219 327 13,132 669 76 149

2010 748 1,406 213 220 327 15,456 667 76 149

2011 759 1,406 215 223 327 15,456 676 76 151

2012 771 1,406 218 226 327 15,456 686 76 153

2013 783 1,406 221 229 327 15,456 697 76 155

2014 796 1,406 224 232 327 15,456 707 76 157

2015 809 1,406 226 235 327 15,456 718 76 159

2016 821 1,406 229 238 327 15,456 729 76 161

2017 833 1,406 232 241 327 15,456 739 76 163

2018 844 1,406 235 243 327 15,456 748 76 165

2019 855 1,406 237 246 327 15,456 758 76 167

2020 866 1,406 240 249 327 15,456 767 76 168

2021 878 1,406 242 251 327 15,456 777 76 170

2022 889 1,406 245 254 327 15,456 787 76 172

2023 901 1,406 248 257 327 15,456 797 76 174

2024 913 1,406 250 260 327 15,456 807 76 176

2025 925 1,406 253 263 327 15,456 817 76 178

2026 937 1,406 256 266 327 15,456 828 76 180

2027 950 1,406 259 269 327 15,456 838 76 182

2028 962 1,406 262 271 327 15,456 849 76 184

2029 975 1,406 265 274 327 15,456 860 76 186

2030 988 1,406 267 277 327 15,456 871 76 188
8 

Numerical Simulation of the Groundwater-Flow System

Groundwater flow in the Chimacum Creek Basin and vicinity was simulated using the 

U.S. Geological Survey modular three-dimensional finite-difference groundwater-flow model, 

MODFLOW-2005 (Harbaugh, 2005). The model described in detail in Jones and others (2013) 

was developed to simulate steady-state conditions. The model is comprised of a grid of 245 

columns and 313 rows; cells are a uniform 200 ft per side. There are six model layers, each 

representing one hydrogeologic unit: (1) Upper Confining unit (UC); (2) Upper Aquifer unit 

(UA); (3) Middle Confining unit (MC); (4) Lower Aquifer unit (LA); (5) Lower Confining unit 

(LC); and (6) Bedrock unit (OE). The boundaries of the model coincide with natural topographic, 

geologic, and hydrologic boundaries except the northern edge, which was located as far north as 

possible without approaching more densely populated areas north of the study area. Three types 

of boundaries were used in the model: specified flux (recharge and pumping wells), headdependent flux (constant head, general head, and drains), and no flow (outer model boundary) 

(Jones and others, 2013, fig. 3). The bottom boundary of the model is a no-flow boundary 

(bottom of layer 6 at an altitude of 1,500 ft below NAVD 88). The areal boundaries along the 

southern edge of the model correspond with the drainage basin boundaries of Chimacum Creek. 

These natural features act as no-flow boundaries as they are considered coincident with 

groundwater divides. 

The steady-state simulation represented average conditions for October 1994–September 

2009, which were used to calibrate the model. The steady-state calibration used as calibration 

targets average groundwater-level measurements in 57 wells (table 2), averaged surface-water 

baseflow measurements at 13 locations (table 3, streamgage 17B050 and 12 other synoptic 

baseflow measurement locations), plus estimated inflows to aquifer layers 2 and 4 through the 

northern boundary of the model. This calibration estimated the hydraulic conductivities of all 

layers, conductances for most boundary conditions, and preliminary stream conductances. For 

the transient calibration, groundwater levels were included for 37 of the wells and 119 surfacewater flow measurements. The groundwater-level measurements were collected monthly during 

2002–03 and 2008–09. The reported depth of the well screen and the well log were used to 

determine the model layer that represented the hydrogeologic unit screened by the well; for the 

small number of wells screened in multiple units, the unit with the larger screened interval was 

assigned. Surface-water baseflow measurements were collected at 13 locations (fig. 1) during 

three synoptic events (June and October 2002 and July 2007) that represent periods of low flow. 

Mean monthly baseflow values also were computed from the streamflow data measured at the 

gage 17B050 (CS14 in fig. 1) near the mouth of Chimacum Creek for October 2002–September

2009. 
9 

Table 2. Wells used in calibration, Chimacum Creek Basin and vicinity, Jefferson County, Washington. 

[Location of wells shown in figure 1. N/A, not applicable]

Local well No. Site identifier Model 

layer

Number 

of 

measurements

Measured 

groundwater 

altitude (ft, 

NAVD 88)

Calibrated 

steadystate water 

level (ft, 

NAVD 88)

Steadystate 

residual 

(ft)

Mean of 

transient 

residuals 

(ft)

Standard 

deviation of 

transient 

residuals 

(ft)

28N/01W-01C01 475712122445901 5 1 265.77 255.34 10.43 12.55 N/A

28N/01W-02A03 475714122452401 5 2 273.17 268.34 4.83 7.77 0.31

28N/01W-03H01 475653122464101 5 1 279.16 273.72 5.44 10.09 N/A

28N/01W-03J01 475640122464501 5 1 286.21 277.80 8.41 13.31 N/A

28N/01W-04R01 475629122480701 2 15 205.56 200.67 4.89 1.76 0.59

28N/01W-05A01 475708122491501 4 1 284.35 273.87 10.48 16.00 N/A

28N/01W-06H01 475656122504501 4 2 385.29 382.42 2.87 9.43 0.04

28N/01W-06J01 475646122503801 4 2 377.69 377.14 0.55 7.46 0.08

28N/01W-10B01 475622122470101 5 2 294.07 298.74 -4.67 1.92 1.37

28N/01W-10E01 475608122474201 5 2 245.74 258.42 -12.68 -6.13 0.52

29N/01E-07M05 480106122440001 3 2 55.93 66.32 -10.39 -9.85 1.84

29N/01E-19G02 475933122432101 5 1 93.74 103.07 -9.33 -11.23 N/A

29N/01E-19P01 475908122433901 5 2 148.85 124.25 24.60 22.83 0.27

29N/01E-28N04 475816122412301 3 2 5.46 21.17 -15.71 -15.75 1.29

29N/01E-29D01 475852122424201 3 1 92.61 89.99 2.62 1.12 N/A

29N/01E-29D02 475851122424101 6 1 32.81 66.41 -33.60 -34.81 N/A

29N/01E-29D03 475852122424301 3 2 108.55 91.97 16.58 15.18 0.56

29N/01E-29D04 475851122424001 6 1 68.52 65.93 2.59 1.39 N/A

29N/01E-29D07 475851122424201 6 2 100.91 68.30 32.61 31.46 0.06

29N/01E-29R01 475815122413201 3 2 17.79 28.84 -11.05 -11.17 1.73

29N/01E-32R02 475728122414601 2 2 45.09 43.29 1.80 1.82 0.57

29N/01E-33E03 475752122411601 3 1 39.45 31.95 7.50 7.62 N/A

29N/01E-33M05 475741122411101 3 2 30.45 28.41 2.04 2.02 1.61

29N/01W-03G02 480211122471301 4 2 75.68 52.91 22.77 21.85 2.06

29N/01W-03R01 480145122464201 4 31 73.76 75.74 -1.98 1.20 1.19

29N/01W-09J01 480105122481401 4 1 287.43 287.26 0.17 -3.01 N/A

29N/01W-10A01 480129122464701 4 2 86.94 86.92 0.02 -0.75 0.35

29N/01W-11L01 480115122455701 4 2 105.36 96.75 8.61 7.73 0.55

29N/01W-11Q01 480101122455101 4 2 92.29 105.39 -13.10 -14.22 0.39

29N/01W-12H01 480118122440901 6 1 80.67 66.61 14.06 13.92 N/A

29N/01W-13M01 480016122451901 5 32 119.92 117.65 2.27 0.02 0.64

29N/01W-15B01 480047122465801 4 34 108.23 106.32 1.91 -0.07 1.04

29N/01W-15R01 480007122465301 4 34 127.85 124.27 3.58 -1.50 3.50

29N/01W-21E01 475942122490101 6 2 624.65 620.90 3.75 4.27 0.82

29N/01W-21E02 475938122490101 6 2 617.36 620.02 -2.66 -2.09 1.20

29N/01W-21J01 475925122475201 5 1 244.47 207.12 37.35 39.58 N/A

29N/01W-22F03 475935122472601 5 2 183.13 175.08 8.05 8.30 1.40
10

Local well No. Site identifier Model 

layer

Number 

of 

measurements

Measured 

groundwater 

altitude (ft, 

NAVD 88)

Calibrated 

steadystate water 

level (ft, 

NAVD 88)

Steadystate 

residual 

(ft)

Mean of 

transient 

residuals 

(ft)

Standard 

deviation of 

transient 

residuals 

(ft)

29N/01W-23F01 475945122460201 5 19 136.68 120.87 15.81 -3.89 1.82

29N/01W-24K03 475926122444101 5 35 132.33 124.18 8.15 -1.05 0.87

29N/01W-26M03 475830122462101 2 1 122.79 132.39 -9.60 -9.64 N/A

29N/01W-27C01 475856122471801 4 2 221.27 206.59 14.68 16.92 0.34

29N/01W-27E01 475851122474401 5 1 173.8 179.48 -5.68 -5.03 N/A

29N/01W-27F01 475844122472501 5 2 177.21 171.08 6.13 6.34 0.79

29N/01W-31B02 475802122510101 4 2 442.95 445.00 -2.05 3.01 0.38

29N/01W-33R02 475720122480401 4 2 248.26 254.57 -6.31 -1.65 0.68

29N/01W-34C01 475801122472601 4 2 185.61 204.76 -19.15 -16.73 0.59

29N/01W-34F01 475758122473001 4 2 242.07 213.03 29.04 31.81 0.33

29N/01W-35J01 475734122453701 5 32 276.41 270.01 6.40 0.22 0.73

29N/01W-35L01 475734122461101 5 1 276.76 262.80 13.96 15.92 N/A

29N/01W-36A01 475807122441701 5 1 150.41 138.65 11.76 10.66 N/A

30N/01W-28F02 480358122483501 4 2 165.56 112.48 53.08 52.94 0.27

30N/01W-28M02 480350122491001 4 2 124.3 116.62 7.68 7.60 0.91

30N/01W-29A01 480411122491501 4 1 141.85 120.45 21.40 21.33 N/A

30N/01W-32G01 480305122495201 4 1 2.69 36.38 -33.69 -33.74 N/A

30N/01W-33N02 480245122490201 4 1 38.95 23.70 15.25 14.57 N/A

30N/01W-34E01 480308122472801 4 1 78.2 38.51 39.69 38.36 N/A

30N/01W-34H01 480306122464201 4 2 8.2 24.66 -16.46 -18.11 0.59
11

Table 3. Flow measurement locations used for calibration, Chimacum Creek Basin and vicinity, Jefferson 

County, Washington. 

Map ID

(see fig. 1) Site location

Number 

of 

measure

-ments

Average 

flow 

measurement 

(ft3/s)

Calibrated 

steadystate flow 

(ft3/s)

Steadystate 

residual

(ft3/s)

Mean of 

transient 

residuals

(ft3/s)

Standard 

deviation of 

transient 

residual

(ft3/s)

CS1 Chimacum Creek, 20 ft 

upstream from sediment basin, 

and 0.8 mi west of Center

3 0.65 0.12 0.52 0.53 0.29

CS3 Chimacum Creek, 50 ft 

downstream from West Valley 

Road, and 0.6 mi northwest of 

Center.

3 2.50 2.52 -0.02 -0.06 0.32

CS4 Chimacum Creek, at Center 

Road bridge, and 1.7 mi north 

of Center

3 2.98 3.79 -0.81 -0.88 0.20

CS5 Chimacum Creek, 100 ft 

downstream from road bridge, 

and 2.4 mi north of Center.

3 4.08 5.15 -1.07 -1.15 0.47

CS6 Naylor Creek, 10 ft upstream 

from weir, 50 ft downstream 

from West Valley Road, and 

2.8 mi north of Center

3 0.24 0.00 0.24 0.24 0.17

CS7 Putaansuu Creek, 10 ft 

downstream from West Valley 

Road, and 0.9 mi southwest of 

Chimacum

3 0.12 0.03 0.09 0.09 0.04

CS8 Chimacum Creek, at Rhody 

Drive bridge, and 0.3 mi west 

of Chimacum

3 3.70 4.73 -1.03 -1.52 1.14

CS9 East Fork Chimacum Creek, 

30 ft upstream from Egg and I 

Road, and 2.0 mi north of 

Beaver Valley

3 0.67 0.03 0.64 0.64 0.06

CS10 East Fork Chimacum Creek, 

upstream from culvert, and 

3.2 mi south of Chimacum

3 1.59 0.15 1.44 1.41 0.17

CS11f East Fork Chimacum Creek, 

Beaver Valley Road, and 

0.3 mi southeast of Chimacum

2 1.24 0.00 1.24 -1.08 1.07

CS12 East Fork Chimacum Creek, 

20 ft downstream from 

Chimacum Road, and 0.6 mi 

north of Chimacum

3 1.21 0.08 1.13 -0.87 0.88

CS13 Chimacum Creek, at PUD 

gage, 50 ft upstream from 

footbridge, 300 ft east of end of 

Hilda Road, 1.2 mi north of 

Chimacum, and at mile 2.3

3 7.14 2.27 4.87 2.13 0.95

CS14 Chimacum Creek, 0.7 mi 

upstream from mouth

84 11.29 7.41 3.88 0.36 8.49
12

The sensitivity of the simulated model output to changes in the parameter value

determines the uncertainty of the estimated parameter values; values are better estimated for 

parameters with a high sensitivity (a large effect on simulated head). In contrast, changing the 

value of parameters with low sensitivity has little effect on the model-calibration process and 

values for these insensitive parameters are not well estimated. 

Values for 189 parameters (that is, pilot points for horizontal and vertical hydraulic 

conductivities, and conductances for general head, drain, and stream boundary conditions) were 

computed in the steady-state calibration. Sensitivities for these parameters were calculated using 

an “identifiability” measure that is included in the PEST procedure (Doherty and Hunt, 2009) 

based on “singular values” and associated vectors that are part of the Singular Value 

Decomposition Assist (SVDA) procedure. These vectors relate each parameter to its influence on 

the objective function; that is the sum of squared weighted errors at all target wells and 

streamflow targets. The resulting identifiability values (square root of the sum of the vector 

components for a given parameter) are shown in Jones and others (2013, fig. 9). The model is 

most sensitive to horizontal conductivities (Kx) in layers 2, 4, and 6 with pilot points in the 

central portion of these units being best identified (>75 percent identifiability) as seen by the 

high values on the left of the Kx2, Kx4, and Kx6 portions of Jones and others (2013, fig. 9). 

The results of the steady-state calibration were assessed by comparing simulated and 

measured groundwater levels and stream baseflows, and by examining the mean and standard 

errors of residuals (difference between measured and simulated values). The minimum standard 

error on the mean between simulated and measured groundwater levels (2.8 ft) based on standard 

error occurred in model layer 5 (Lower Confining unit LC); the maximum standard error (8.9 ft) 

occurred in model layer 6 (Bedrock unit, OE). Model layers 2 and 3 (UA and MC) had the 

lowest absolute value of mean residuals, indicating simulated groundwater levels in these units 

had the lowest model bias (Jones and others, 2013, table 7). Simulated steady-state groundwaterlevel altitudes in UA indicate flow generally moving down the valleys to the north from the 

drainage divide. Simulated steady-state groundwater-level altitudes in LA indicate flow 

generally moving down valley from the drainage divide to discharge in Discovery Bay, Port 

Townsend Bay, and Oak Bay. A groundwater divide occurs midway between Discovery Bay and 

Port Townsend Bay. Simulated steady-state groundwater-level altitudes in LC indicate flow 

generally moving down valley from the drainage divide toward the groundwater divide that 

occurs midway between Discovery Bay and Port Townsend Bay. 

Baseflow discharge is reasonably well simulated by the steady-state calibration except for 

the East Fork Chimacum Creek. On average, the model underpredicts the amount of baseflow in 

the East Fork of Chimacum Creek and at two locations downstream of the confluence between 

Chimacum Creek and the East Fork (sites CS13 and CS14). This is likely due to the humic bogs 

present along the East Fork (locally known as “Magical Dirt”), which drain slowly giving the 

recession curve a logarithmic shape similar to one affected by large amounts of bank storage. 

This is evidenced by the dark brown color of the water in the reach during the summer months as 

the humic bogs slowly discharge to the creek.
13

Transient Calibration

Transient groundwater flow represents a dynamic system, in which variable inflows, 

outflows, and groundwater storage change with time. A calibration to transient conditions was 

performed which incorporated monthly variations in recharge and discharge. Transient 

conditions for calibration were simulated for October 1994–September 2009 using 180 monthly 

stress periods. During model calibration, variables were adjusted within probable ranges to 

minimize differences between measured and simulated groundwater levels and stream baseflows. 

The transient version of the model proved inherently unstable and was not used to simulate 

alternate hydrologic or anthropogenic changes. 

The model was calibrated in a two-step process, first using steady-state simulations to 

estimate hydraulic conductivities of the six model layers to match measured heads and flows at 

target wells and streamflow sites, then using a transient simulation to estimate the parameters 

that predominantly affect fluctuations in flow, storage coefficients, and stream conductance. 

Calibrated values from the steady-state analysis were then used in attempts to calibrate the model 

using transient conditions, which included adjusting stream conductances and storage 

coefficients. Each transient stress period consists of three timesteps. Calibration of the transient 

simulation yielded estimates of storage coefficients in the upper layers, and estimates for stream 

conductance. 

All model layers were simulated as confined units so that the transmissivity of each cell 

remained constant throughout the duration of the simulation. This simplification improved the 

numerical stability of the model. Although model layers 1–3 were simulated as confined, they 

are in reality largely unconfined, therefore, during the calibration process, storage coefficients 

were allowed to be as high as 0.5, to allow values that would be representative of specific yield 

values. Where model layers were conceptually confined, storage coefficients were assigned the 

value of 2.0(10)-6 ft-1. 

The initial time step in this transient analysis was based on a steady-state condition that 

simulates average recharge, discharge, and groundwater levels for predevelopment conditions 

(no anthropogenic development). The transient simulation period (October 1994–September 

2009) was divided into 180 monthly stress periods to represent temporal variations in recharge, 

discharge, and storage. Agricultural groundwater withdrawals were apportioned between May 

and September, as was done for the surface-water diversions. Attempts to calibrate the transient 

model used head and flow data measured from October 2001 through September 2009 to 

estimate storage coefficients for (conceptually) unconfined model layers, and stream 

conductances for 33 stream reaches. 
14

The model calibration used nonlinear regression with the parameter-estimation program 

PEST, with regularized inversion (Doherty, 2003, 2005), pilot points to represent heterogeneity 

of aquifer and confining unit properties, and SVDA. This approach allowed a relatively large 

number of parameters (189 parameters for the steady-state calibration and 97 for the transient 

case) to be estimated using a set of pilot points distributed throughout the model domain 

(Doherty, 2003, 2005). Hydraulic properties of each hydrogeologic unit within the model were 

then estimated through spatial interpolation using kriging from the pilot points to the model grid 

cells. The result is a smooth variation of the hydraulic property values within the model domain. 

A number of studies have described the use of pilot points for groundwater-model 

calibration. Twenty-six pilot point locations were evenly spread throughout the model domain 

and were distributed vertically so that each hydrogeologic unit contained pilot points. Pilot points 

were not specified where a hydrogeologic unit was absent. Twenty pilot points were used for 

both hydraulic conductivity and storage coefficients with the remaining six pilot point locations 

added to estimate storage coefficients. Because not all pilot point locations had all hydrogeologic 

units present, it resulted in 150 active hydraulic conductivity pilot points (75 for Kx and 75 for 

Kz) and 32 pilot points for storage coefficients for (conceptually) unconfined conditions (see 

Jones and others, 2013, fig. 8). 

The final values for calibration parameters are listed in table 4 and the areal distribution 

of horizontal and vertical conductivities are shown in Jones and others (2013, fig. 8A-L). The 

properties of layer 2 (Upper Aquifer unit, UA) are the dominant variables (vertical and 

horizontal hydraulic conductivity) and the properties of model layer 4 (Lower Aquifer unit, LA) 

are similarly significant. Model layers 1 (Upper Confining unit, UC) and 3 (Middle Confining 

unit, MC) have the highest values of storage coefficients (fig. 3A-F). 
15

Table 4. Final values for calibration parameters. 

Kh (ft/d) 

Model 

layer

Number of 

active cells Geomean Minimum Maximum Change from initial estimate

Median 

thickness (ft)

1 3,136 0.375 0.002 32.04 × 0.38 30

2 9,150 167.6 0.436 498.8 × 10.1 <5

3 25,035 0.396 0.001 47.62 × 0.49 51

4 21,795 1.627 0.01 489.6 × 0.48 62

5 28,966 0.152 1.0(10)- 5 103.0 × 0.06 274

6 44,775 0.08 7.0(10)- 6 10.9 × 0.42 1,476

Kv (ft/d) 

Model 

layer Geomean Minimum Maximum Change from initial estimate

1 6.27 4.04 10 × 1.13

2 17.9 0.427 50 × 0.69

3 0.184 7.6(10)- 5 4.94 × 0.64

4 6.69 0.751 43.3 × 0.64

5 0.73 5.5(10)- 5 10 × 0.71

6 0.165 4.9(10)- 4 0.977 × 1.37

Specific Storage (1/ft), for cells with unconfined conditions

Model 

layer

Number of cells 

with unconfined 

conditions

Geomean Minimum Maximum Change from initial 

estimate

1 3,136 0.0563 0.0343 0.13 × 0.28

2 6,273 0.124 0.0497 0.20 × 0.62

3 24,839 0.159 0.0561 0.49 × 0.79

4 3,350 0.122 0.099 0.14 × 1.0(10)5

5 9,088 0.111 0.044 0.33 × 1.0(10)5

6 7,712 0.0482 0.0134 0.078 × 4.8(10)4

Note: All cells with confined conditions were set at specific storage of 2.0(10)-6. 

Drain Conductance (ft2/d) 

Drain 

group Application Final value Change from initial estimate

0 Small streams, shallow bedrock 1,000 × 0.043

1 Coastal seeps 25,852 × 1.63
16

Table 4. Final values for calibration parameters.—Continued

GHB Conductance (ft2

/d)

GHB

group Application Final value Change from initial estimate

0 Model boundaries in Puget Sound 907.7 × 0.00087

1 Lakes 5.34(10)8 × 28.6

2 North boundary in Unit 2 100 Not in previous model

4 North boundary in Unit 4 1.532(10)5 Not in previous model

Stream Conductance (ft2/d)

Stream reach Final value Change from initial 

estimate

1 3.2 × 0.298

2 66.0 × 0.207

3 763 × 77.2

4 96,612 × 764

5 0.37 × 0.0148

6 1,140 × 0.170

7 0.36 × 0.0006

9 0.87 × 0.0044

11 3,769 × 1.261

12 389 × 6.83

14 378,883 × 22.8

15 2,028 × 41.1

16 10.2 × 0.494

17 2.61 × 1.208

19 3,311 × 22.1

20 330 × 3.33

22 145 × 6.71

23 110.7 × 4.18

24 529 × 2.90

25 2,881 × 10.15

26 66,233 × 4.02

27 55.2 × 8.07

28 74.7 × 0.109

29 14.6 × 5.38

31 56,467 × 216

32 53.3 × 0.569

34 270,211 × 143.7

35 23,717 × 28.3

37 6,543 × 148.7

38 711 × 7.61

39 15,439 × 13.17

40 11,589 × 178.3

41 8.77 × 0.481
17

A. Layer 1; Upper Confining unit (UC).

Figure 3. Maps showing areal distribution of storage coefficient values, with shading indicating where the 

storage coefficient is specified as confined, and locations of storage coefficient calibration pilot points for all 

model layers, Chimacum Creek Basin and vicinity, Jefferson County, Washington. 
18

B. Layer 2; Upper Aquifer unit (UA). 

Figure 3.—Continued.
19

C. Layer 3; Middle Confining unit (MC). 

Figure 3.—Continued.
20

D. Layer 4; Lower Aquifer unit (LA). 

Figure 3.—Continued.
21

E. Layer 5; Lower Confining unit (LC)

Figure 3.—Continued.
22

F. Layer 6; Bedrock unit (OE).

Figure 3.—Continued.
23

The transient calibration was complicated by persistent instability problems apparently 

caused by large variations in groundwater exchange with surface water between iterations of the 

solver. This resulted in long execution times and elevated residual estimates. The transient model 

proved inherently unstable. Due to temporal transitions from gaining reaches (groundwater 

discharging to the stream) to losing reaches (surface water recharging the aquifer), the model 

would not converge for any timestep, and could only be calibrated using a solution algorithm 

(pcgN) that would allow for non-convergence at any particular timestep and proceed to the next. 

No timesteps converged. 

Calibrated groundwater level altitudes in the target wells agree on average with their 

measured values in a similar fashion to what was seen in the results of the steady-state 

calibration (fig. 4, table 5). The model as calibrated to transient conditions has a mean residual 

and standard error of 0.06 ft ± 0.45 ft for heads and 0.48 ± 0.06 ft3/s for flows. The mean and 

standard errors of the mean residuals are smaller in magnitude (less than 1 ft) for all layers

except in MC and OE, as well as overall, lower than those from the steady-state calibration and 

scaled by the range of measured values, the standard errors for all model layers (except model 

layer 3, MC) were less than 3 percent. 

Figure 4. Graph showing simulated and measured groundwater-level altitudes for the calibrated model for 

transient conditions, Chimacum Creek Basin and vicinity, Jefferson County, Washington. 
24

Table 5. Calibration statistics for the transient calibration by hydrogeologic unit and baseflow, Chimacum Creek Basin and vicinity, Jefferson County, 

Washington. 

[Abbreviations: ft, feet; ft2

, square feet; NA, not applicable]

Hydrogeologic unit 

observation group

Count of 

observations

Mean of 

residuals 

(ft)

Standard error 

of residuals 

(ft)

Mean of 

absolute values 

of residuals (ft) 

Objective 

function 

(sum of 

squared 

residuals) 

(ft2) 

Range of 

measured 

values

(ft) 

Standard error 

of residual / 

Range of 

observations 

(percent)

Heads in UC (model layer 1) 0 

Heads in UA (model layer 2) 18 1.13 0.65 2.20 151 44.66 – 202.25 0.4 

Heads in MC (model layer 3) 10 -3.91 3.75 10.79 1,420 4.50 – 109.05 3.6 

Heads in LA (model layer 4) 133 1.89 0.92 5.22 15,477 2.69 – 443.17 0.2 

Heads in LC (model layer 5) 140 0.52 0.48 2.72 4,493 39.45 – 295.04 0.2 

Heads in OE (model layer 6) 9 5.31 6.65 13.97 3,434 32.81 – 625.23 1.1 

Total: All heads 310 1.16 0.50 4.35 24,975 2.69 – 625.23 0.1 

Baseflow observations, in 

cubic feet per second

119 0.23 (ft3

/s) 0.66 (ft3

/s) 4.56 (ft3

/s) 6047 (ft3

/s)2 0.1 – 44.4 (ft3/s) 1.5 
25

Observed fluctuations are small (mostly 2 ft, but range from 0.5 to 9 ft) compared to the 

value of the average groundwater level (due to altitude and flow gradients), so variations are not 

obvious in the scatter plot (fig. 4). The hydrographs (figs. 5A and 5B) do show simulated 

fluctuations in groundwater level, but these fluctuations were not reproduced in the transient 

calibration to the magnitude shown in the measured values. To show the fluctuations in 

groundwater levels more clearly in the hydrographs, the scale for the simulated data (left axis) 

are shifted relative to the measured data (right axis) but both are shown to the same scale.

Simulated groundwater levels show the expected seasonal trend—higher groundwater 

levels in the late winter to lowest levels in the late summer in the few wells with sufficient 

measurements (for example, fig. 5B, wells 29N/01W-03R01 and 29N/01W-15R01, both in LA; 

and wells 29N/01W-13M01, 29N/01W-23F01, and 29N/01W-24K03, all in LC). There also is a 

multi-year fluctuation in a few wells with high groundwater levels in about 1999, and again in 

about 2006. The highest annual precipitation recorded at the NWS station Chimacum 4 S during 

the calibration period (1995–2009) were in 1999 (43.31 in.) and 2006 (35.29 in.).

The transient calibration also attempted to fit the baseflow measurements in the 

Chimacum Creek system. The standard deviation of the 119 observations was about 1.5 percent 

of the range of measurements (table 5). A comparison between simulated and measured 

streamflows are shown in figure 6. The highest simulated flows are 33 percent of the measured

flows at the most downstream site (CS14). Low flows were less well estimated. Hydrographs for 

the measurements and simulations are shown in figure 7. The more upstream locations show the 

same simulated seasonal fluctuation that reflects groundwater level seasonal fluctuations—it can 

be seen in the measured flow but only at the gage where the most data are available (site CS14). 

However, also apparent in the flow hydrographs for the downstream sites (CS11f, CS12, CS13, 

and CS14) is a fluctuation that reflects the problematic instability of the transient model. These 

instabilities can be shown to arise in the cells near CS11f, downstream of the largest diversion. 
26

Figure 5. Hydrographs (A) and expanded hydrographs for selected wells (B) of simulated and measured 

groundwater-level altitudes for the calibrated model for transient conditions, Chimacum Creek Basin and 

vicinity, Jefferson County, Washington. 
27

Figure 5A.—Continued.
28

Figure 5A.—Continued.
29

Figure 5A.—Continued.
30

Figure 5A.—Continued.
31

Figure 5A.—Continued.
32

Figure 5A.—Continued.
33

Figure 5A.—Continued.
34

Figure 5A.—Continued.
35

Figure 5A.—Continued.
36

Figure 5B.—Continued.
37

Figure 5B.—Continued.

Figure 6. Graph showing simulated and measured streamflow from groundwater discharge for the 

calibrated model for transient conditions, Chimacum Creek Basin and vicinity, Jefferson County, 

Washington. 
38

Figure 7. Hydrographs of simulated and measured streamflow from groundwater discharge for the 

calibrated model for transient conditions, Chimacum Creek Basin and vicinity, Jefferson County, 

Washington. 
39

Figure 7.—Continued.
40

Figure 7.—Continued.
41

Figure 7.—Continued.

Possible Causes for Poor Calibration

MODFLOW attempts to solve the governing equations of groundwater flow where the 

unknown variables (groundwater-level altitude, streamflow, hydraulic conductivity, etc.) are 

more numerous than the known variables. Because of this, MODFLOW, as well as other 

groundwater- flow models, estimates values for variables, calculates the difference between 

variables and target values, and adjusts the value of the variable(s) in an iterative process to 

minimize the difference, or “residual.” The model repeats the process, “iterates,” until the 

differences are minimized; it “converges” on the minima. The magnitude of acceptable residuals 

is set as part of model preparation, and attaining results at or lower than the value set is called 

convergence. In a steady-state simulation, this process is done once; in a transient simulation, 

this process is repeated for each of the time intervals (“time steps”), which together cover the 

entire time period being considered. The transient simulation failed to converge for any time

steps, with the largest residuals occurring primarily during the time periods representing late 

summer, when Chimacum Creek would have lowest flows and would be receiving groundwater 

discharge in the largest amounts during the course of a year, and for the longest lengths of a 

stream. The information provided by the model from a failed convergence is limited to the 

magnitude of changes in heads and residuals for model cells, and the largest of those occurred in 

cells representing Chimacum Creek. Therefore, it is presumed that the instability and failure to 

converge is due to aquifer- stream interactions. The MODFLOW STR package was used to 

simulate cells representing Chimacum Creek, and as part of the solution for each time step, 

stream stages and cumulative streamflow are estimated. Those estimates of stream stage and 

cumulative streamflow cascade to downstream cells, further increasing the potential for 

developing numerical instabilities. Thus, it appeared that oscillation between gaining and losing 

conditions in Chimacum Creek, and the associated cascade of these changes from upstream to 

downstream, were the primary cause of the failure to achieve a successful transient calibration. 

Streamflow loss to groundwater when the water table is below the bottom of the stream channel

is a linear function of stream stage. Streamflow loss to groundwater when the water table is 

above the bottom of the stream but below the stream stage, and streamflow gain from 
42

groundwater are functions of both the water-table altitude and the stream stage, both of which the 

model is attempting to estimate. This was possibly the cause of the numerical instability, which

prevented convergence. 

Recommendations for Further Study

Although the MODFLOW package STR was considered necessary in order to efficiently 

simulate and calculate cumulative stream stages and streamflow, which was a calibration target, 

an alternative package such as RIV could possibly be used with adapted calibration targets that 

would allow convergence during the calibration process. RIV would not attempt to estimate (and 

thus, vary) the stream stage, and would not cascade those estimates and changes of those 

estimates between iterations downstream. The resulting model would perhaps not be as useful as 

one successfully calibrated using STR, but it may eliminate the instabilities that caused the 

failure to converge experienced using STR. Additionally, alternate methods of formulating and 

solving the governing equations in newer versions of MODFLOW, such as MODFLOW-NWT, 

could be used to attempt to achieve a successful calibration. 

Summary 

A steady-state groundwater-flow model was developed to evaluate potential future 

impacts of growth and of water-management strategies on water resources in the Chimacum 

Creek Basin. The model, the steady-state calibration, and simulation of potential future

conditions are reported in Scientific Investigations Report 2013-5160, Numerical Simulation of 

the Groundwater-Flow System in Chimacum Creek Basin and Vicinity, Jefferson County, 

Washington. The model covers an area of about 64 square miles on the Olympic Peninsula in 

northeastern Jefferson County, Washington. The Chimacum Creek Basin drains an area of about 

53 square miles and consists of Chimacum Creek and its tributary East Fork Chimacum Creek, 

which converge near the town of Chimacum and discharge to Port Townsend Bay near the town 

of Irondale. The geologic setting for Chimacum Creek Basin and the adjacent lands to the west, 

bordering Discovery Bay, and to the east, bordering Port Townsend Bay and Oak Bay, are 

typical of the Puget Sound Lowlands; unconsolidated deposits of glacial and interglacial origin 

are present throughout the study area. Recharge from precipitation is the dominant source of 

water to the aquifer system. Return flow (recharge resulting from water use) from irrigation and 

septic systems contribute small amounts of recharge. Discharge primarily is to marine waters 

below sea level and to Chimacum Creek and its tributaries. Springs, seeps, and wells for public 

supply, domestic supply, and agriculture comprise the balance of groundwater discharge. 

The model is comprised of a grid of 245 columns and 313 rows; cells are a uniform 200 

feet per side. There are six model layers, each representing one hydrogeologic unit: (1) Upper 

Confining unit (UC); (2) Upper Aquifer unit (UA); (3) Middle Confining unit (MC); (4) Lower 

Aquifer unit (LA); (5) Lower Confining unit (LC); and (6) Bedrock unit (OE). The boundaries of 

the model coincide with natural topographic, geologic, and hydrologic boundaries except the 

northern edge. The transient simulation period (October 1994–September 2009) was divided into 

180 monthly stress periods to represent temporal variations in recharge, discharge, and storage. 

Agricultural groundwater withdrawals were apportioned between May and September, as was 

done for the surface-water diversions. Attempts to calibrate the transient model used head and 

flow data measured from October 2001 through September 2009 to estimate storage coefficients 

for (conceptually) unconfined model layers, and stream conductances for 33 stream reaches. 
43

The attempt to calibrate the model to transient conditions was unsuccessful due to 

instabilities stemming from oscillations in groundwater discharge to recharge from streamflow in

Chimacum Creek. The model as calibrated to transient conditions has a mean residual and 

standard error of 0.06 ±0.45 feet for heads and 0.48 ±0.06 cubic feet per second for flows. 

Measured fluctuations in groundwater levels were small, typically about 2 feet; similar 

fluctuations were not observed in the transient simulation, although the expected seasonal 

fluctuations were observed. The highest simulated streamflows were 33 percent of the measured

flows at the most downstream station. Low flows were less well estimated. Because the transient 

version of the model proved inherently unstable, it was not used to simulate forecast conditions 

or alternate hydrologic or anthropogenic changes.

Alternate stream simulation packages, such as RIV, could be used to simulate Chimacum 

Creek in order to achieve an acceptable calibration, although the utility of the resulting model 

might be less useful than a successful calibration using the package used for this attempt (STR). 

Additionally, newer versions of MODFLOW, such as MODFLOW-NWT, could prove capable 

of managing the instabilities resulting from highly varying groundwater/surface-water 

interactions. 

References Cited

Doherty, J., 2003, Ground water model calibration using pilot points and regularization: Ground 

Water, v. 41, no. 2, p. 170–177. 

Doherty, J., 2005, PEST—Model-independent parameter estimation: Corinda, Australia, 

Watermark Numerical Computing, variously paged. 

Doherty, J., and Hunt R.J., 2009, Two statistics for evaluating parameter identifiability and error 

reduction: Journal of Hydrology, v. 366, no. 1–4, p. 119–127 

Harbaugh, A.W., 2005, MODFLOW-2005, the U.S. Geological Survey modular ground-water 

model—The ground-water flow process: U.S. Geological Survey Techniques and Methods 6-

A16, variously paged. 

Jones, J.L., Johnson, K.H., and Frans, L.M., 2013, Numerical simulation of the groundwaterflow system in Chimacum Creek Basin and vicinity, Jefferson County, Washington: U.S. 

Geological Survey Scientific Investigations Report 2013-5160, 79 p. (Also available at 

http://pubs.usgs.gov/sir/2013/5160.) 

Jones, J.L., Welch, W.B., Frans, L.M., and Olsen, T.D., 2011, Hydrogeologic framework, 

groundwater movement, and water budget in the Chimacum Creek basin and vicinity, 

Jefferson County, Washington: U.S. Geological Survey Scientific Investigations Report 2011–

5129, 28 p. (Also available at http://pubs.usgs.gov/sir/2011/5129/.) 

National Oceanic and Atmospheric Administration, 2007, Climatological data—Annual 

summary, Washington: Asheville, North Carolina, National Climatic Data Center, v. 111, no. 

13, 30 p. 

Parametrix, Inc., Pacific Groundwater Group, Inc., Montgomery Water Group, Inc., and 

Caldwell and Associates, 2000, Stage 1 technical assessment as of February 2000, Water 

Resource Inventory Area (WRIA) 17: Jefferson County, Washington, Project No. 553-1820-

007, accessed July 28, 2011, at 

http://www.ecy.wa.gov/programs/eap/wrias/Planning/docs/063010_wria17_water_supply_de

mand.pdf. 

Ritter, D.F., 1978, Process geomorphology: Dubuque, Iowa, William C. Brown Company 

Publishers, 414 p. 
44

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ISSN 2331-1258 (online)

http://dx.doi.org/10.3133/ofr20131258

Jones and Johnson—Transient Calibration of a Groundwater-Flow Model of Chimacum Creek Basin and Vicinity, Jefferson County, Washington—Open-File Report 2013-1258