U.S. Department of the Interior

U.S. Geological Survey

Open-File Report 2016–1135

Prepared in cooperation with the Naval Facilities Engineering Command–Northwest

Numerical Simulation of Groundwater Flow at 

Puget Sound Naval Shipyard, Naval Base Kitsap, 

Bremerton, Washington

Numerical Simulation of Groundwater Flow at Puget 

Sound Naval Shipyard, Naval Base Kitsap, Bremerton, 

Washington

By Joseph L. Jones, Kenneth H. Johnson, and Lonna M. Frans

Prepared in cooperation with the Naval Facilities Engineering Command-Northwest

Open-File Report 2016–1135

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, Director

U.S. Geological Survey, Reston, Virginia: 2016

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Suggested citation: 

Jones, J.L., Johnson, K.H., and Frans, L.M., 2016, Numerical simulation of groundwater flow at Puget Sound Naval 

Shipyard, Naval Base Kitsap, Bremerton, Washington: U.S. Geological Survey Open-File Report 2016-1135, 3 p., 

http://dx.doi.org/10.3133/ofr20161135. 

ISSN 2331-1258 (online)
iii

Contents

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

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

Background............................................................................................................................................................. 2

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

Previous Work ......................................................................................................................................................... 3

Description of the Shipyard and Surrounding Area ................................................................................................. 5

Groundwater-Flow System ......................................................................................................................................... 8

Geologic Setting...................................................................................................................................................... 8

Hydrogeologic Units................................................................................................................................................ 9

Hydraulic Conductivity........................................................................................................................................... 10

Conceptual Model of Groundwater Flow............................................................................................................... 11

Numerical Simulation of the Groundwater-Flow System........................................................................................... 13

Spatial Discretization............................................................................................................................................. 13

Boundary Conditions and Implementation of MODFLOW Packages .................................................................... 14

Recharge Package............................................................................................................................................ 14

Drain Package ................................................................................................................................................... 14

General-Head Boundary Package..................................................................................................................... 16

Horizontal-Flow Barrier Package....................................................................................................................... 16

Model Calibration .................................................................................................................................................. 16

Calibration Procedure........................................................................................................................................ 16

Calibration Data................................................................................................................................................. 17

Final Parameter Values and Sensitivities .......................................................................................................... 17

Assessment of Steady-State Calibration ........................................................................................................... 19

Model Limitations .................................................................................................................................................. 22

Model Applications.................................................................................................................................................... 23

Water Budget ........................................................................................................................................................ 23

Simulation of Particle Tracking.............................................................................................................................. 24

MODPATH Procedure....................................................................................................................................... 24

Summary .................................................................................................................................................................. 28

References Cited...................................................................................................................................................... 29

Figures

Figure 1. Map showing location of study area, Puget Sound Naval Shipyard, Naval Base Kitsap, 

Bremerton, Washington ............................................................................................................................................. 6

Figure 2. Map showing recharge to model cells in the active domain, Puget Sound Naval Shipyard, 

Naval Base Kitsap, Bremerton, Washington............................................................................................................ 12

Figure 3. Example cross-section showing hydrogeologic units and model cells along column 55 .......................... 13

Figure 4. Map showing boundary conditions for the groundwater flow model, Puget Sound Naval Shipyard, 

Naval Base Kitsap, Bremerton, Washington............................................................................................................ 15

Figure 5. Graph showing simulated and measured water-level altitudes for the groundwater flow model, 

Puget Sound Naval Shipyard, Naval Base Kitsap, Bremerton, Washington ............................................................ 20

Figure 6. Map showing water-level residuals and water-level contours for layer 6 for the groundwater flow 

model, Puget Sound Naval Shipyard, Naval Base Kitsap, Bremerton, Washington ................................................ 21
iv

Figure 7. Map showing forward particle tracking from selected model cells within the shipyard for the 

groundwater flow model, Puget Sound Naval Shipyard, Naval Base Kitsap, Bremerton, Washington .................... 26

Figure 8. Map showing backward particle tracking from long-term monitoring wells for the groundwater flow 

model, Puget Sound Naval Shipyard, Naval Base Kitsap, Bremerton, Washington ................................................ 27

Tables

Table 1. Final parameter values and sensitivities for the groundwater flow model, Puget Sound 

Naval Shipyard, Naval Base Kitsap, Bremerton, Washington.................................................................................. 18

Table 2. Water budget for steady-state groundwater conditions for the groundwater flow model, 

Puget Sound Naval Shipyard, Naval Base Kitsap, Bremerton, Washington ............................................................ 23

Table 3. Wells, measured water level altitudes, and model cell assignments used in calibration............................ 32

Conversion Factors

Multiply By To obtain

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

inch (in.) 2.54 centimeter (cm)

inch (in.) 25.4 millimeter (mm)

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

mile (mi) 1.609 millimeter (mm)

foot (ft) 0.3048 meter (m)

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

square mile (mi2) 2.590 square kilometer (km2) 

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

°F=(1.8×°C)+32. 

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), referred to in this report as “sea 

level.”

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

Altitude, as used in this report, refers to distance above or below sea level.
1 

Numerical Simulation of Groundwater Flow at Puget 

Sound Naval Shipyard, Naval BaseKitsap, Bremerton, 

Washington

By Joseph L. Jones, Kenneth H. Johnson, and Lonna M. Frans

Abstract 

Information about groundwater-flow paths and locations where groundwater discharges at and 

near Puget Sound Naval Shipyard is necessary for understanding the potential migration of subsurface 

contaminants by groundwater at the shipyard. The design of some remediation alternatives would be 

aided by knowledge of whether groundwater flowing at specific locations beneath the shipyard will 

eventually discharge directly to Sinclair Inlet of Puget Sound, or if it will discharge to the drainage 

system of one of the six dry docks located in the shipyard. A 1997 numerical (finite difference) 

groundwater-flow model of the shipyard and surrounding area was constructed to help evaluate the 

potential for groundwater discharge to Puget Sound. That steady-state, multilayer numerical model with 

homogeneous hydraulic characteristics indicated that groundwater flowing beneath nearly all of the 

shipyard discharges to the dry-dock drainage systems, and only shallow groundwater flowing beneath 

the western end of the shipyard discharges directly to Sinclair Inlet.

Updated information from a 2016 regional groundwater-flow model constructed for the greater 

Kitsap Peninsula was used to update the 1997 groundwater model of the Puget Sound Naval Shipyard. 

That information included a new interpretation of the hydrogeologic units underlying the area, as well as 

improved recharge estimates. Other updates to the 1997 model included finer discretization of the finitedifference model grid into more layers, rows, and columns, all with reduced dimensions. This updated 

Puget Sound Naval Shipyard model was calibrated to 2001–2005 measured water levels, and hydraulic 

characteristics of the model layers representing different hydrogeologic units were estimated with the 

aid of state-of-the-art parameter optimization techniques. 

The flow directions and discharge locations predicted by this updated model generally match the 

1997 model despite refinements and other changes. In the updated model, most groundwater discharge 

recharged within the boundaries of the shipyard is to the dry docks; only at the western end of the 

shipyard does groundwater discharge directly to Puget Sound. Particle tracking for the existing longterm monitoring well network suggests that only a few wells intercept groundwater that originates as 

recharge within the shipyard boundary. 
2 

Introduction

The Puget Sound Naval Shipyard (PSNS) Complex Superfund site, generally referred to as 

either the Bremerton Naval Complex or as Naval Base Kitsap Bremerton (in this report, Puget Sound 

Naval Shipyard, or just “shipyard”) lies on the northern shore of Sinclair Inlet in Puget Sound. The 

shipyard has a long history that includes extensive filling along the shoreline to create a landscape

amenable to industrial activity. The fill is comprised of construction and demolition debris, concrete 

rub/le, culverts, waste metal, and other unidentified fill materials. This study was undertaken to update 

an existing model (Prych, 1997) with new hydrogeologic interpretation and recharge estimates, and 

greater spatial resolution. 

Background

The industrialized portion of the Puget Sound Naval Shipyard in Bremerton, Washington, has 

been involved in Naval shipbuilding and repair activities since the 1890s. Information about 

groundwater-flow paths and locations where groundwater discharges near the shipyard is necessary for 

understanding the fate and transport of subsurface contaminants, which at this site include various 

volatile organic compounds including trichloroethene (commonly referred to as TCE) and 

tetrachloroethene (or perchloroethylene, commonly referred to as PCE). Five of the six large ship dry 

docks along the shoreline of the site are heavily pumped to remove inflow, creating local cones of 

depression that significantly alter groundwater head gradients, effectively capturing groundwater 

contaminants from a wide area but also increasing groundwater velocities and thus minimizing travel 

times for natural attenuation. Potential offsite sources of groundwater contamination also may be 

captured by dry dock pumping. The current remediation strategy or future remediation plans that may be 

enacted as new contaminants are discovered would benefit from a better understanding of how 

groundwater-flow paths and discharge zones are affected by increased development of the site (URS 

Consultants, Inc., 1994a).

In July 2012, the U.S. Geological Survey (USGS), in cooperation with Naval Facilities 

Engineering Command-Northwest, began a project to construct and apply a groundwater flow model for 

the area of PSNS to better understand the historical and potential future migration of VOCs in 

groundwater. An existing steady-state USGS MODFLOW groundwater-flow model (Prych, 1997) was 

(1) rediscretized to enhance the spatial resolution by approximately a factor of two; (2) updated with 

land-use information and recharge boundary conditions that reflect changes to the extent of industrial 

areas; (3) made consistent with the newly interpreted hydrogeologic framework for a regional 

groundwater-flow model constructed for the greater Kitsap Peninsula in 2016 (Frans and Olsen, 2016), 

and (4) calibrated using new groundwater-level data with the benefit of the parameter estimation 

program (PEST) (Doherty, 2005, 2006). 
3 

Purpose and Scope

This report describes the construction, calibration, and application of an updated MODFLOW 

groundwater-flow model for the PSNS. The model is based on a previous model (Prych, 1997), with the 

addition of hydrogeologic interpretation of the underlying strata, and decreased cell dimensions 

throughout. Recharge values used by Prych (1997) were recalculated to be consistent with those used 

for the regional-scale Kitsap Peninsula model (Welch and others, 2014), based on precipitation, surficial 

geology, and land cover, with further refinements to accommodate smaller cell sizes and to better reflect 

land cover (particularly impervious areas). Model particle-tracking applications were used to describe 

overall flow paths within the groundwater-flow system as simulated, and to estimate the contributing 

recharge area associated with selected monitoring wells. 

The report does not address transient (time-varying) conditions such as seasonal variations in 

groundwater recharge or tidal fluctuations, nor does it discuss the possible influences of these variables 

under transient conditions. 

Previous Work

An initial assessment of contamination and physical features and ecology of the shipyard and 

surrounding area was conducted under the CLEAN program (U.S. Navy, 1983), which identified six 

potentially contaminated sites at the shipyard. A preliminary assessment supplemental report (U.S. 

Navy, 1990) identified five additional sites. Eight of the 11 sites were recommended for inclusion in a 

site-inspection study. The site-inspection study, which was the first major study of the shipyard under 

the CLEAN program, included 12 sites (URS Consultants, Inc., 1992a). As part of the site inspection 

study, information on stratigraphy and contaminants in soil was collected by boring 79 holes and 

collecting and analyzing soil samples from the holes. Wells for measuring water levels and collecting 

water samples were installed in 30 of the holes, and slug tests for estimating horizontal hydraulic 

conductivity were conducted on 26 of the wells. 

A number of individual or groups of sites (called Operable Units) that were the subject of the 

site-inspection study also have been the subject of numerous follow-up studies (URS Consultants, Inc., 

1993a, 1993b, 1993c, 1993d, and 1994b). Most of these studies were conducted to collect additional 

information on the hydrogeology and degree and extent of contamination in order to determine the 

human and environmental health risks posed by the contaminants, to decide if remediation work is 

necessary, and to evaluate the feasibility of different remediation alternatives. 

URS Consultants, Inc. (1992b) described a numerical model of groundwater flow and solutetransport in the shipyard and immediate area that was constructed to evaluate effects of general 

groundwater flow, tidal action, and saltwater intrusion on the fate and transport of subsurface 

contaminants. This model was constructed using the finite-difference computer code HST3D (Kipp, 

1987), which is capable of simulating non-steady flow of a fluid with a nonuniform density. The 

modeled area was digitized on an 11 × 17 rectangular grid of points in each of two layers. Model 

simulations indicated that much of the groundwater at the shipyard flows to the drainage systems of the 

dry docks. However, because the dimensions of a model cell were about as large or larger than the 

dimensions of a typical dry dock, the model was not capable of resolving details of groundwater flow to 

individual dry docks, except for perhaps to dry dock 6 (DD-6), which is more than 1,000 ft from the 

other dry docks. Simulations with and without tides indicated that tides do not affect groundwater-flow 

directions farther than about one grid space (about 700 ft) inland from the shoreline. Simulated 

groundwater levels were 0 to 0.81 m (0–2.7 ft) higher with the density of water in Sinclair Inlet greater 

than the density of fresh groundwater than with the density of water in Sinclair Inlet equal to the density 

of fresh groundwater. 
4 

During summer 1994, Prych (1995) measured the quantity and quality of water flowing into and 

out of the dry docks. Prych used these measurements to estimate the rates of fresh and saline 

groundwater discharge into each dry dock. These discharges were used to assess the numerical 

groundwater model of the present study. 

A second Remedial Investigation/Feasibility Study RI/FS, for Operable Unit (OU) A, was 

initiated by the Navy in 1993. Two field investigations were conducted from April to June 1993 and 

from June to September 1994. The final OU A RI report was published in August 1995 (U.S. Navy, 

1995b). The final FS was published in October 1995 (U.S. Navy, 1995c). The Record of Decision for 

OU A was signed in January 1997 (U.S. Navy, Washington State Department of Ecology, and U.S. 

Environmental Protection Agency, 1997). 

Remedial Investigations (RIs) for OU NSC (March 1993–September 1994, U.S. Navy, 1995a) 

and OU B (March–July 1994; U.S. Navy, 1996) included collection of groundwater samples from 8 and 

31 locations, respectively. These included salinity profiles. A second RI at OU B included collection of 

groundwater samples from 47 locations during July–November 1995, and 8 locations in July 1995 (URS

Consultants, Inc., 2002). 

OU B was divided into separate terrestrial and marine units in spring 2000; a final RI report 

addressing OU B Terrestrial was published in March 2002 (URS Consultants, Inc., 2002). OU C is a 

petroleum unit being managed under the State of Washington’s cleanup program, rather than CERCLA. 

A steam sparging system was installed at OU C in 1996 and was used until 1998 to recover petroleum 

product (U.S. Navy, 2002a, 2004). System operation was terminated in response to decreasing product 

recovery rates. Quarterly monitoring of groundwater in downgradient wells was initiated in January 

2001. A Cleanup Action Plan for OU C was approved by the Washington State Department of Ecology 

(2007). OU D was created in August 2002 comprising a limited portion of the far eastern end of OU B 

Terrestrial (U.S. Navy, 2004). 

Long-term monitoring results (Sealaska, 2015, 2016) include descriptions of the current 

monitoring wells’ construction details, as well as analytical results from ongoing sampling, and trends 

for contaminant concentrations. The areas that contribute recharge to these wells, and whether the wells 

are likely to intercept recharge that has passed through known contaminant sources is of ongoing 

interest. 

The model described herein is a revision of the model described in Prych (1997), which covered

the same area with a steady-state model comprising 14 layers, 70 rows, and 40 columns. Grid 

dimensions for the Prych model ranged from 125 to 1,000 ft in the north-south direction and from 47 to 

600 ft in the east-west direction, with the smallest dimensions near the dry docks. Layer thickness 

ranged from 10 to 1,650 ft with the thinnest layers located between 90 ft below to 12 ft above sea level, 

which includes the dry docks. The layers were homogeneous with horizontal hydraulic conductivity of 

10-3 ft/s, and vertical hydraulic conductivity of 10-7 ft/s. 

The water budget for the Prych model with no-flow boundaries on the model perimeter showed 

discharge to the dry docks was more than twice the estimated recharge from precipitation, with the 

balance flowing into the dry docks from Puget Sound. Discharge to Puget Sound was less than one-third 

of recharge from precipitation. Results using specified-head boundaries were similar. Particle-tracking 

results for the model were used to delineate recharge areas with common discharge areas; with the 

exception of the western edge of the shipyard, all particles discharged at one of the five dry docks with 

drainage systems. 
5 

Welch and others (2014) described the hydrogeologic framework, groundwater movement, and 

water budget of the Kitsap Peninsula, including the area occupied by the shipyard. Building on that

work, Frans and Olsen (2016) described the groundwater movement and water budget of the Kitsap 

Peninsula based on computer modeling. The calibration of that model used water levels from 2007 to 

2012. Hydraulic head contours for aquifers were created with steady-state simulations. 

Description of the Shipyard and Surrounding Area

Naval Base Kitsap was created in 2004 by merging the former Naval Station Bremerton with 

Naval Submarine Base Bangor. The mission of Naval Base Kitsap is to serve as the host command for 

the Navy’s fleet throughout western Puget Sound and to provide base operating services, including 

support for both surface ships and submarines homeported at Bremerton and Bangor. The area of 

interest in this study is the PSNS, which occupies a strip of land as wide as 0.6 mi wide that stretches 

along 1.8 mi of the northern shore of Sinclair Inlet near its mouth, and the offshore area where 

groundwater from the shipyard may discharge into Sinclair Inlet (fig. 1). The modeled area also includes 

near-offshore areas and most of the peninsula occupied by the city of Bremerton in order to provide the 

model with suitable hydrologic boundaries. 
6 

Figure 1. Map showing location of study area, Puget Sound Naval Shipyard, Naval Base Kitsap, Bremerton, 

Washington. 
7 

The peninsula upon which the shipyard and the city of Bremerton are located is about 3 mi long 

in the east-west direction and about 2 mi wide in the north-south direction, and is part of the larger 

Kitsap Peninsula. The peninsula is bordered on the south, east, and north by various bays and inlets of 

Puget Sound. Land-surface altitudes on the peninsula range from sea level to a maximum of about 240 ft 

above sea level on north-south trending hills that form a drainage divide on the western side of the 

peninsula. Land-surface altitudes east of these hills are mostly between 50 and 150 ft. Nearly all land on 

the peninsula has been developed, and the entire peninsula is served by public-water supplies and a 

sanitary sewer system, and many areas have storm drains. There are no perennial streams on the 

peninsula. 

Sinclair Inlet is deepest near its mouth, where it is about 70 ft deep at mean tide. The inlet is 

shallowest at its western end, where large mud flats are exposed at low tide. Typical depths in front of 

the piers and dry docks of the shipyard are about 45 ft, and typical depths in Port Washington Narrows 

on the eastern side of the peninsula are about 30 ft. Tides in Puget Sound and Sinclair Inlet are diurnal, 

with two unequal high and two unequal low tides during each tidal cycle (about 24.8 h). The mean tide 

range (difference between mean lower low and mean higher high water) is about 12 ft. Salinity of the 

water in the inlet is typically about 30 parts per thousand, but it varies a few parts per thousand both 

spatially and temporally. Stratification of saline water is slight, probably because no large freshwater 

streams discharge to the inlet or elsewhere nearby to Puget Sound. 

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

Temperatures are moderated by the Pacific Ocean and Puget Sound. The ocean provides an abundant 

supply of moisture for winter storms that typically approach the area from the southwest. Mean annual 

precipitation (average annual precipitation for 1981–2010) is 56.4 in. at Bremerton (National Oceanic 

and Atmospheric Administration, 2014). The distribution of precipitation varies throughout the year at 

Bremerton. Summers (June–August) are typically dry with a mean total precipitation of 3.8 in. and 

winters (December–February) are wetter than summers with a mean total precipitation of 25 in. Mean 

monthly temperature (average monthly temperature for 1981–2010) at Bremerton ranges from about 

40°F in December to about 66°F in August (National Oceanic and Atmospheric Administration, 2014).
8 

Groundwater-Flow System

This section describes the hydrogeologic units that constitute the groundwater-flow system in 

the model area and includes discussions of recharge, flow directions, and discharge to dry docks. This 

information was used to construct and calibrate the numerical model and is based on the work of Prych 

(1997), Welch and others (2014), Frans and Olsen (2016), and information provided by the Naval 

Facilities Engineering Command-Northwest. 

Geologic Setting

The shipyard and surrounding area are located in the Puget Sound Lowlands, a north-south 

trending structural basin that is partly filled with unconsolidated glacial and interglacial deposits. The 

most recent advance and retreat of continental glaciers in the Pleistocene epoch of the Quaternary 

Period left behind more than 3,000 ft of unconsolidated deposits in the Puget Lowland (Jones, 1996). 

The Puget Lobe of the Cordilleran ice sheet advanced and retreated several times into the Puget 

Lowland from the mountains of British Columbia during the Pleistocene and left behind a complex 

sequence of alternating glacial and interglacial sediments. The Vashon Stade of the Fraser Glaciation 

was the most recent and extensive of the major advances. Glacial sediment typically includes (in order 

of deposition) outwash sand and gravels deposited by the advancing ice; glacial till (hard and poorly 

sorted mixture of clay, silt, sand, and gravel) and ice-contact material deposited beneath and adjacent to 

the ice; and outwash sand and gravels at the top of the sequence deposited by the retreating ice. 

Each major glacial interval was followed by an extended interglacial period during which 

fluvial, lacustrine, bog, and marsh deposition dominated. Interglacial deposits typically comprise clay, 

silt, or discontinuous lenses of sand and gravel or peat. Underlying the unconsolidated glacial and 

interglacial deposits in the Puget Lowland are Tertiary bedrock units comprised mainly of sedimentary 

and volcanic rocks. 

Total thickness of glacial and interglacial deposits near the shipyard ranges from 0 to about 

1,800 ft (Jones, 1996). The most common geologic units exposed at land surface in the Bremerton area 

are Vashon till and outwash. Bedrock (marine and non-marine sedimentary rocks and volcanic rocks) is 

exposed at land surface about 2 mi north of the shipyard and also in another area about 2 mi west of the 

shipyard. In addition to the natural sediments, a large part of the industrial area of shipyard is built on 

fill that is as much as 50 ft thick near the shoreline (URS Consultants, Inc., 1994a). The fill consists of 

construction and demolition debris, other waste material, and natural sediments from nearby 

excavations. A low-permeability unit consisting mostly of early Vashon glaciolacustrine silt and clay is 

present beneath the fill.
9 

Hydrogeologic Units

Hydrogeologic units, consisting of aquifers and confining units were defined for this study on 

the basis of lithologic (depositional facies, grain size, and sorting) and hydrologic (hydraulic 

conductivity and unit geometry) characteristics (Welch and others, 2014). Glacial deposits generally are 

heterogeneous, and although a glacial aquifer may be composed primarily of sand or gravel, it locally 

may contain varying amounts of clay or silt. Conversely, a confining unit composed predominantly of 

silt or clay may contain local lenses of coarse material. 

Unconfined and confined conditions are present in the groundwater-flow system and affect the 

movement and storage of groundwater in the study area. Unconfined conditions occur when the upper 

surface of the saturated zone (water table) is at atmospheric pressure and the water table is free to rise 

and decline, filling and draining pore space, respectively, in response to changes in groundwater 

recharge and discharge. Confined conditions occur when groundwater pressure exceeds atmospheric 

pressure due to the presence of a less permeable overlying unit that constrains the thickness of the 

saturated zone. Transient changes in fluid pressure or head under confined conditions in response to 

groundwater recharge and discharge are governed by the compressibilities of the fluid and the skeletal 

matrix of the hydrologic units and do not result in filling or draining pore space. 

Ten hydrogeologic units are recognized in the study area including bedrock, which is modeled as 

a no-flow boundary; their lithologic and hydraulic characteristics are described below.

• The Vashon till confining unit (Qvt) is present at land surface throughout much of the study 

area. This low-permeability unit is composed of a dense mix of sand and gravel in a clay matrix. 

The unit is absent at land surface in some areas due to erosion by ephemeral streams. The

average thickness of Qvt within the active model boundary is 42 ft. 

• The Vashon advance aquifer (Qva) consists of well-sorted sand, or sand and gravel, with 

lenses of silt and clay that underlies the Qvt, and also is exposed at the surface at several 

locations. Confined groundwater conditions are present where the unit is saturated fully and is 

overlain by Qvt, and unconfined conditions are present at locations where the Qva is exposed at 

land surface. The average thickness of Qva within the active model boundary is 65 ft.

• Beneath Qva is the upper confining unit (QC1), which is a thick and laterally extensive lowpermeability unit consisting mostly of early Vashon glaciolacustrine silt and clay (Kitsap Clay) 

and underlying interglacial deposits of silt, sand, and gravel with numerous lenses of silt and 

clay or silty peat. The average thickness of QC1 within the active model boundary is 91 ft. 

• The sea-level aquifer (QA1) is present in the subsurface throughout the study area and consists 

primarily of glacial sand and gravel, with silt interbeds. There are no surface exposures of QA1 

within the study area, and groundwater in this aquifer is under confined conditions. The average 

thickness of QA1 within the active model boundary is 99 ft. 

• The middle confining unit (QC2) is a low-permeability unit underlying QA1, consisting of 

interglacial sandy silty clay and glacial sand and gravel, with significant amounts of silt and clay 

layers. The unit is present in the subsurface throughout the study area, and the average thickness 

of QC2 within the active model boundary is 136 ft.
10 

• The glaciomarine aquifer (QA2) is present in the subsurface throughout the study area and 

ranges in composition from sand and gravel to silt, with occasional shell fragments. There are no 

surface exposures of QA2 in the study area, and groundwater in this aquifer is under confined 

conditions. The average thickness of QA2 within the active model boundary is 161 ft.

• The lower confining unit (QC3) is a low-permeability unit composed of clay and silt, with 

some gravel. The unit is present in the subsurface throughout the study area, and the average

thickness of QC3 within the active model boundary is 165 ft. 

• The deep aquifer (QA3) is present in the subsurface throughout the study area and consists 

primarily of sand and gravel with silt interbeds. There are no surface exposures of QA3 within 

the study area, and groundwater in this aquifer is under confined conditions. The average 

thickness of QA3 within the active model boundary is 170 ft.

• The basal confining unit (QC4) is a low-permeability unit composed of clay and silt with some 

gravel. The unit is present in the subsurface throughout the study area, and the average thickness 

of QC4 within the active model boundary is 271 ft.

• Bedrock (BR) is present in the subsurface throughout the study area and consists of marine and 

non-marine sedimentary rocks and volcanic rocks. The bedrock unit crops out in the northern 

part of the study area. 

In addition to the hydrogeologic units, a large part of the shipyard is built on artificial fill. Welch 

and others (2014) did not map this areally small Fill unit for the regional Kitsap model, instead mapping 

the unit as QC1 in that area. A Fill unit was added to the updated model constructed in this study by 

converting appropriate QC1 cells in the regional model into Fill cells in the updated model. The areal 

extent of the Fill unit was taken from P.J. Hauessler (U.S. Geological Survey, unpub. data, 2007). The 

Fill unit was assigned to model layers from the ground surface down through layer 7. 

Hydraulic Conductivity

Welch and others (2014) reported median estimated horizontal hydraulic conductivities for 

hydrogeologic units based on specific-capacity data from well drillers’ reports, and Frans and Olsen

(2016) reported median model-generated hydraulic conductivities for the hydrogeologic units within the 

Kitsap Peninsula study area. Those values, respectively, are, in feet per day (-- indicates not reported): 

Qvt (--, 3.14), Qva (51, 24.57), QC1 (--, 0.83); QA1 (38, 12.26); QC2 (--, 0.98); QA2 (35, 7.90); QC3 (-

-, 0.81); QA3 (32, 19.64). These values were used to aid in evaluating model-calibrated conductivity 

estimates. 
11 

Conceptual Model of Groundwater Flow

Recharge to the groundwater-flow system occurs primarily due to infiltration of natural 

precipitation; in this model, recharge from other sources such as outdoor use of domestic water is

considered negligible. The long-term average annual precipitation at Bremerton, Washington, is 56.37 

in/yr for 1981–2010 (Welch and others, 2014). Areally distributed precipitation amounts were used by 

Welch (2014) along with surficial geology (glacial outwash or glacial till) and land cover (with tree 

canopy, without tree canopy, or urban/bedrock) using the regression equations developed by Bidlake 

and Payne (2001) to calculate estimated mean annual recharge from precipitation for use in the regional 

Kitsap peninsula groundwater-flow model (Frans and Olsen, 2016). Those values were re-discretized to 

match the cell sizes used in this updated PSNS model (fig. 2). Regional groundwater flow also enters 

into the model area from the west; the magnitude of this flow was estimated using output from the 

Kitsap Peninsula model (Frans and Olsen, 2016). 

Groundwater-flow directions are reflective of the general topography of the model area—from 

the high ground to the west and north, southeastward toward Sinclair Inlet and Port Washington 

Narrows. Prych (1997) contoured measured water levels to demonstrate that the dry docks locally 

capture southeast-trending flow as discharge to the dry-dock drains. 

The dry docks generally are drained except when flooded to float a vessel. Dry docks 1 and 3 

through 6 are equipped with drains on the sides and headwall and beneath the bottom to remove any 

groundwater that seeps in, and their bottom altitudes range from -16.5 ft (dry dock 3) to -45.5 ft (dry 

dock 6). Such a large altitude difference between the dry-dock bottom and the surrounding terrain 

creates steep groundwater potentiometric head gradients that alter the natural groundwater-flow 

directions; the gradients are steep toward the dry docks (except dry dock 2), which causes groundwater 

in the immediate vicinity of a dry dock to flow directly to that dry dock. Prych (1997) used forward 

particle-tracking analyses to demonstrate that “nearly all groundwater flowing through the shipyard 

discharges to the drainage systems of the dry docks.” 
12 

Figure 2. Map showing recharge to model cells in the active domain, Puget Sound Naval Shipyard, Naval Base 

Kitsap, Bremerton, Washington. 
13 

Numerical Simulation of the Groundwater-Flow System 

This revision of the Prych steady-state model with updated areal recharge and inflow from the 

regional flow system, hydrogeology, and cell and layer dimensions also was calibrated to steady-state 

conditions; in this case, measured hydraulic heads for 2001–2005. The model used was MODFLOWNWT (Niswonger and others, 2011). 

Spatial Discretization

The geographic extent of the updated numerical finite-difference model is the same as that 

defined by Prych (1997), but the number of model rows is increased from 70 to 104, and the number of 

columns is increased from 40 to 141. Ranges in row heights are reduced from 125-1,000 ft to 55-240 ft. 

Ranges in column widths are reduced from 47-600 ft to 26-300 ft. 

The updated model includes 22 layers compared to Prych’s (1997) 14 model layers, and the tops 

or bottoms of the updated model layers are redefined so that each layer lies within a single 

hydrogeologic unit. Overall, the nine natural hydrogeologic units plus the fill unit were divided into 22 

layers, with the uppermost hydrogeologic units having the most model layers; figure 3 shows a northsouth cross section of the model showing hydrogeologic unit assignments and cell boundaries. 

Figure 3. Example cross-section showing hydrogeologic units and model cells along column 55. 
14 

Boundary Conditions and Implementation of MODFLOW Packages 

Boundary conditions (fig. 4) were applied to model cells to represent conditions at locations 

where water enters or exits the groundwater-flow system. This model of the Puget Sound Naval 

Shipyard uses several MODFLOW packages (Niswonger and others, 2011) to represent these 

conditions: the Recharge Package for areal groundwater recharge due to precipitation; the General Head

Boundary (GHB) Package for groundwater discharge to marine water, and groundwater inflow at the 

western edge of the active model domain; the Drain Package for groundwater discharge to the six dry 

docks, and in areas where low hydraulic conductivity units outcrop and route groundwater to the land 

surface; and the Horizontal-Flow Barrier package (HFB) (Hsieh and Freckleton, 1993) to represent 

impediments to groundwater discharge from sheet-pile cutoff walls and concrete bulkheads. No-flow 

cells were used in the interior of the dry docks as they are empty space. Additionally, because the model 

is within the domain of a groundwater model of the Kitsap Peninsula (Frans and Olsen, 2016), 

simulated hydraulic heads from the Kitsap model were used with the GHB Package to help define 

groundwater inflow at the western edge of the active model domain where Prych (1997) used surfacewater divides to infer no-flow boundaries. The model was assigned no-flow boundaries on the bottom of 

the model domain (beneath QC4, representing bedrock). Figures 2 and 4 show the distribution of the 

various boundary condition cells. 

Recharge Package

The Recharge Package (RCH) of MODFLOW was used to simulate areal groundwater recharge 

from precipitation. Recharge (in units of feet per day) was applied as a specified flux to the uppermost 

active cell. Precipitation is the dominant source of water recharging the groundwater system in the study 

area, and variations in recharge are related to spatial and temporal variations in precipitation, the 

permeability of surficial hydrogeologic units, and land-cover characteristics. The distribution of annual 

recharge from precipitation in the study area (Welch and others, 2014) was estimated by applying 

precipitation-recharge relations based on regression equations developed for areas in Puget Sound, 

Washington (Bidlake and Payne, 2001) that incorporate the effects of surficial hydrogeology and tree 

canopy characteristics. Using those equations, the groundwater system received an average (1980–2010) 

of 7.53 in. of recharge from precipitation annually. 

Drain Package

The model simulates groundwater discharge to the dry-dock drainage systems from model cells 

that are adjacent to dry-dock sidewalls or headwalls and from cells beneath dry-dock floors using the 

Drain Package of MODFLOW. The drain altitude for a cell adjacent to a dry-dock wall is assumed 

equal to the altitude of the mid-point of the cell, whereas the drain altitude for a cell beneath a dry-dock 

floor is assumed to equal the altitude of the top of the concrete floor. Drains also were placed in areas 

where low hydraulic conductivity units outcrop at the surface to simulate the routing of rejected 

recharge in those areas.
15 

Figure 4. Map showing boundary conditions for the groundwater flow model, Puget Sound Naval Shipyard, Naval 

Base Kitsap, Bremerton, Washington. 
16 

General-Head Boundary Package

Cells in contact with salt water (along Sinclair Inlet and Port Washington Narrows) are cells that 

conceptually discharge more, or less, groundwater depending on the relative heads of the groundwater 

system at the cell and the equivalent fresh-water head of salt water at that location. The General Head 

Boundary (GHB) package provides the capability to simulate this head-dependent flow, and is applied 

at all cells in contact with salt water. The specified head for model cells representing the sea floor in 

Puget Sound was set to fresh-water equivalent heads (above sea level). Freshwater equivalent heads 

above sea level were set equal to 0.023 times the height of the saltwater column above the cell (van 

Heeswijk and Smith, 2002, p. 39). 

GHB cells also were used along the western edge of this model to allow groundwater inflow 

across boundary cells where Prych (1997) used no-flow conditions assuming surface-water divides 

could reasonably infer a groundwater divide. Hydraulic head values were specified in these GHB cells 

using output from regional model of the Kitsap Peninsula (Frans and Olsen, 2016). 

Horizontal-Flow Barrier Package

The sheet-pile cutoff walls beneath the dry docks and the subsurface parts of shoreline bulkheads 

impede the horizontal flow of groundwater. This phenomenon is simulated by using the HorizontalFlow Barrier (HFB) Package (Hsieh and Freckleton, 1993). HFBs increase the resistance to horizontal 

flow between two adjacent cells in a layer. HFBs were placed in the model at the locations of the 

bulkheads and cutoff walls shown in Prych (1997). 

Model Calibration 

Model calibration is the adjustment of model parameter values within limits so that the 

differences (residuals) between measured and simulated groundwater levels are minimized with respect 

to an objective function, here, the sum of squared weighted residuals. Calibration is assessed by 

examining how well simulated match measured water-level altitudes.

Calibration Procedure

The model was calibrated using a combination of traditional trial-and-error adjustment of 

parameter values and the Parameter ESTimation program (PEST) (Doherty, 2005, 2006). PEST was 

used to adjust the values of the model parameters (horizontal and vertical hydraulic conductivities of 

each hydrogeologic unit; and drain, HFB, and GHB conductances) between model calibration runs 

repeatedly until the differences in measured and simulated water-level altitudes attain minimal sum of 

squared weighted residuals. Parameter values were constrained within PEST similar to the bounds given 

to the larger regional Kitsap model. During the calibration process, trial and error was used to establish 

five Fill units each with homogenous conductivities that allowed the best fit for the water level data.

Pilot points and zonation were not used; the Fill units are similar to zones but modeled as individual 

hydrogeologic units with uniform conductivities.
17 

Calibration Data

The model was calibrated to best simulate average measured water-level altitudes in monitoring 

(non-pumping) wells that were measured during 2001–2005. There were 170 wells in 152 unique model 

cells. Of these model cells, 118 were assigned to the Fill (layers 4–7), 11 cells were assigned to Qva 

(layers 1–10), 16 to QC1 (layers 4–12), 5 to QA1 (layers 11–14), and 2 to QC2 (layers 15–16). 

Measured water-level altitudes ranged from 37.38 to -56.82 ft (table 3, at back of report).

Each of the water-level altitudes was assigned a weight. Weights are assumed to be proportional 

to the inverse of the standard deviation of the measurement error (Doherty, 2005; Hill and Tiedeman, 

2007), which is problematic to quantify for wells used in this study due to differing or inconsistent datacollection methods and documentation of variables such as land-surface altitude or vertical datum. Some 

land-surface altitudes were necessarily defaulted to the LiDAR land-surface altitude used for the model, 

which was obtained through the Puget Sound LiDAR Consortium (2000). Weightings, therefore, were 

assigned using professional judgment on a scale from 0.25 to 10, with PEST using the values as relative 

inverse weights. Accurate, repeated observations, with little variation of water-level altitude were 

assigned a value of 10; wells with greater variability were assigned values of 4.5, and wells with few 

measurements or comparatively large variability, were assigned 3. Weighting values of 1, 0.5, and 0.25 

were used for wells with high variability. 

Final Parameter Values and Sensitivities

The ability to estimate a parameter value during the calibration process is related to the

sensitivity of simulated hydraulic head to changes in the parameter value. For example, if a parameter 

has a high sensitivity, the observation data effectively estimate the parameter value. For parameters with 

low sensitivity, changes in the parameter value have little effect on the model-calibration process.

Insensitive parameters may or may not be close to their corresponding field values and are not likely to 

be estimated accurately during the parameter-estimation process. 

Relative composite sensitivities are a measure of composite changes in model outputs that are 

caused by small changes in the value of a modeled parameter (Doherty, 2005). For a given modeled 

parameter, the larger the value of the associated relative composite sensitivity, the more sensitive the 

model is to that parameter. Relative composite sensitivities were calculated and analyzed for all

parameters used in the model-calibration process (table 1). The parameters with the highest sensitivities 

were the horizontal and vertical hydraulic conductivities of the Qva and QC1 units, and the horizontal 

conductivity of Fill unit 3.
18 

Table 1. Final parameter values and sensitivities for 

the groundwater flow model, Puget Sound Naval 

Shipyard, Naval Base Kitsap, Bremerton, 

Washington. 

Parameter Value Sensitivity

Horizontal hydraulic conductivity, in feet per day

Qvt 3.99068 8.87 × 10-2

Qva 29.0836 1.01

QC1 0.203648 0.978

QA1 1,000 0.60

QC2 5.60 × 10-5 1.92 × 10-5

QA2 0.358813 3.44 × 10-2

QC3 1.22 × 10-4 2.34 × 10-5

QA3 2.04916 1.51 × 10-6

QC4 4.81 × 10-2 9.49 × 10-6

Fill 1 5,088.16 0.38

Fill 2 313.274 2.39 × 10-2

Fill 3 13.2424 0.94

Fill 4 100 0.32

Fill 5 10,000 1.68 × 10-2

Vertical hydraulic conductivity, in feet per day

Qvt 0.40 7.34 × 10-3

Qva 2.37 × 10-2 0.74

QC1 5.78 × 10-2 1.28

QA1 100 5.17 × 10-2

QC2 2.43 × 10-3 4.62 × 10-2

QA2 0.10 7.57 × 10-4

QC3 1.90 × 10-6 1.78 × 10-4

QA3 1.44 1.84 × 10-5

QC4 0.103811 1.51 × 10-6

Fill 1 11.06 2.47 × 10-3

Fill 2 1.15 × 10-2 0.49

Parameter Value Sensitivity

Fill 3 1.00 × 10-6 1.22 × 10-3

Fill 4 11.31 2.46 × 10-3

Fill 5 0.39 6.92 × 10-2

Drain conductance, in feet per day

Surface drains 100 2.42 × 10-4

Dry dock 1 85,000 4.42 × 10-3

Dry dock 3 8,419.14 2.99 × 10-3

Dry dock 4 1.00 × 106 2.52 × 10-4

Dry dock 5 1.00 × 106 4.84 × 10-4

Dry dock 6 1.00 × 106 3.11 × 10-3

General head boundary conductance, in feet per day

Puget Sound 1.52 × 108 2.53 × 10-5

Qvt 0.25 3.82 × 10-3

Qva 4.98 × 10-2 3.43 × 10-3

QC1 53.123 0.47

QA1 1.96 1.21 × 10-2

QC2 7.19 × 10-4 2.33 × 10-5

QA2 12.95 1.32 × 10-2

QC3 15.29 2.03 × 10-5

QA3 780.8 0.32

QC4 6.44 01.15 × 10-5

Horizontal flow barrier conductance, in feet per day

HFB 2.47 × 10-8 4.95 × 10-5
19 

Assessment of Steady-State Calibration

The results of the calibration were assessed by examining the mean and the root mean‐square 

error (RMSE) of the difference of measured and simulated water-level altitudes (residuals). The mean of 

residuals represents the average difference between all measured and simulated values (residuals), and 

the sign of the mean of residuals (bias) indicates whether the model is over- or under-predicting values 

(negative and positive mean of residuals, respectively). The RMSE of weighted residuals provides a 

measure of variation that considers measurement accuracy. The RMSE of the difference between 

simulated and measured hydraulic heads in the observation wells, divided by the total range in water 

levels in the groundwater system (Anderson and Woessner, 1992, p. 241), also should be less than 10 

percent to be considered acceptable (Drost and others, 1999). 

The final calibration resulted in a mean residual value of 1.15 ft, indicating the model slightly 

underpredicts water-level altitudes for the area. Given that the total range of average measured 

groundwater levels is 94.2 ft, the final calibration RMSE of 9.08 ft is 9.6 percent of the total range. The

RMSE divided by the total range of values is less than 10 percent, indicating an acceptable model fit

(Drost and others, 1999). 

A plot of measured and simulated groundwater-level altitudes provides a useful graphical 

assessment of model calibration (fig. 5). Measured and simulated values should plot close to a line with 

a slope of 1.0 and an intercept of zero. This diagonal line represents perfect agreement between

measured and simulated values (line of equal measured and simulated values), and the magnitude of the 

residual (difference between measured and simulated values) is reflected in the distance of the value 

above or below the line. Positive residuals (measured value is greater than simulated value) and negative 

residuals (measured value is less than simulated value) plot below and above the line, respectively. 

Measured and simulated values are shown in figure 5. The model did not simulate the exceptionally 

high or exceptionally low measured values well. 

The results of the calibration also were evaluated by displaying the simulated water levels 

(heads) spatially (fig. 6), along with the residuals for each well. Simulated water-level altitudes indicate 

that the model reasonably simulated groundwater conditions, and the spatial distribution of the residuals 

does not indicate any major patterns of bias. 
20 

Figure 5. Graph showing simulated and measured water-level altitudes for the groundwater flow model, Puget 

Sound Naval Shipyard, Naval Base Kitsap, Bremerton, Washington
21 

Figure 6. Map showing water-level residuals and water-level contours for layer 6 for the groundwater flow model, Puget Sound Naval Shipyard, 

Naval Base Kitsap, Bremerton, Washington.
22 

Model Limitations

A groundwater-flow model is a simplification of a complex natural system with a set of 

mathematical equations that describe the groundwater-flow system. Intrinsic to the model is the error 

and uncertainty associated with the approximations, assumptions, and simplifications that must be 

made. Hydrologic-modeling errors typically are the consequence of a combination of (1) input data, (2) 

representation of the physical processes by the algorithms of the model, and (3) parameter estimation 

during the calibration procedure (Troutman, 1985). Examples of model errors and how those errors limit 

application of the model include: 

1. Input data on types and thicknesses of hydrogeologic units, water levels, and hydraulic 

properties represent only approximations of actual values. Model-discretization errors (including 

effects of averaging altitude information over the model cell size) result from inaccuracies in the 

geometric representation of hydrogeologic units, in the representation of the aquifer areas and 

their contact with adjacent units, and from potentially unmapped discontinuities in layer extents 

or properties, as might result from localized geologic disturbances such as landslides, stream 

channels, or fault zones. The physical processes within a groundwater-flow system cannot be 

represented completely in a numerical model. Determining if a weakness in a simulation is 

attributable to input data error or model shortcomings is almost impossible, but the simplifying 

assumptions and generalizations that are incorporated into a model undoubtedly affect the results 

of the simulation. Deriving useful insight from added model complexity requires good constraint 

on the properties and processes being added, but in the absence of such knowledge a simplified 

model will provide a more generalized result.

2. Errors in parameter estimates occur when improper values are selected during the calibration 

process. Various combinations of parameter values can result in low residual error, yet 

improperly represent the actual system. An acceptable degree of agreement between simulated 

and measured values does not guarantee that the estimated model-parameter values uniquely and 

reasonably represent the actual parameter values. The use of nonlinear regression and associated 

statistics, such as composite scaled sensitivities and correlation coefficients, removes some of 

the effects of non-uniqueness, but does not eliminate the problem entirely. Aquifer properties 

will vary within a geologic unit in a way not captured by calibration schemes that assume 

uniform values for each hydrogeologic layer. 

If the numerical simulation is used appropriately, the effects of the simplifications and other 

potential errors can be minimized. If the model is used for simulations beyond which it was designed, 

however, the generalizations and assumptions used could significantly affect the results. 
23 

Model Applications

Water Budget

An approximate steady-state groundwater budget for the study area is expressed as:

Rppp + GGii = D (1)

where

Rppt is recharge from precipitation, 

GWin is groundwater or seawater flowing into the study area, and

D is discharge.

Sources of groundwater in the study area include recharge from precipitation and groundwater 

inflow from the west. Discharge from the system occurs as seepage to seepage faces; drainage to the dry 

docks; and as submarine seepage to Puget Sound. 

 A more detailed representation of the groundwater budget of the study area is: 

Rppp + GGii = Dss + DPP + Ddd (2)

where

 

Dsw is discharge to surface drains, 

DPS is discharge to Puget Sound, and 

Ddd is discharge to the dry docks. 

Total simulated flow through the groundwater system is 19.70 ft3/s (table 2). Recharge accounts 

for 2.47 ft3/s of inflow to the study area and groundwater inflow accounts for 17.23 ft3/s. Discharge 

from the entire model domain is primarily through discharge to Puget Sound, and secondarily to the dry 

docks. Discharge to Puget Sound accounts for 15.34 ft3/s of outflow and discharge to the dry docks 

accounted for 4.36 ft3

/s. The simulated discharge to the dry docks is less than the 8.65 ft3/s of 

groundwater discharge measured by Prych (1995). However, simulated discharge is within the estimated 

accuracy of 30–50 percent for the measured discharge to dry docks. 

Table 2. Water budget for steady-state groundwater conditions for the groundwater flow model, Puget Sound Naval 

Shipyard, Naval Base Kitsap, Bremerton, Washington. 

[Data are in cubic feet per second] 

Inflow Rate Outflow Rate

Recharge from precipitation (Rppt) 2.47 Discharge to surface drains (Dsw) 3.66 × 10-3

Groundwater inflow (GWin) 17.23 Discharge to Puget Sound (DPS) 15.34

Discharge to dry docks (Ddd) 4.36

Total 19.70 19.70
24 

Simulation of Particle Tracking

 MODPATH (Pollock, 1994) is a particle-tracking post-processing package that was developed 

to compute three-dimensional flow paths using output from groundwater-flow simulations by 

MODFLOW. In this study, MODPATH version 5.0 was used for both forward and backward tracking 

of particles. Particle tracking is useful because it can indicate the flow path of a conservative (nonreactive) solute (“particle”) transported in groundwater given a starting location (forward tracking) such 

as the water table or a contaminated location. It can also indicate where a “particle” may have originated 

given a specific ending location (backward tracking). Thus, general flow patterns and discharge areas 

simulated by a groundwater model can be depicted, and capture areas may be estimated. 

MODPATH Procedure

The computer model MODPATH uses a semi-analytical, particle-tracking scheme. The method 

is based on the assumption that each directional-velocity component (calculated from MODFLOW 

output) varies linearly within each model cell. This assumption allows an analytical expression 

describing the flow path within each cell to be obtained using the simulated flows through the faces of 

the cell. The velocity of groundwater is affected by the porosity of the material through which the 

groundwater is flowing. Specified porosities for layers in the updated model were 0.2 for the Qvt unit; 

0.3 for the Fill, Qva, QA1, and QA2 units; and 0.4 for the QC1, QC2, QC3, and QC4 units, based on 

published values for similar geologic units (Fetter, 1994). Given the initial position of a particle, the 

position of the particle at any future time can be calculated. A series of calculations for successive 

locations of a particle provide a simulated particle path through the model domain. See Pollock (1994) 

for a detailed discussion of the particle-tracking procedure. 

MODPATH can run either a forward simulation or a backward simulation. Both were run in this 

study. MODPATH requires the initial locations of the particles to be specified as to which cell, and how 

many particles are to be tracked from that cell. Particles may be placed on cell faces or edges. In a 

forward simulation, initial particle locations within or on the faces and (or) edges of model cells are 

specified and particle paths are calculated from those starting points to where the particles discharge 

from the model domain. In a backward simulation, particle ending locations (such as a monitoring well 

or dry-dock drain) are specified on the faces and(or) edges of the model cell in question, and a particle 

path is calculated from that ending point backward to where the particle entered the model domain. 

In the forward simulation, particles were released at the start of the steady-state stress period at 

the water table in every fifth cell in every fifth row (one particle per 25 cells) within the shipyard 

boundary and tracked forward to their discharge points. The resulting particle paths provide a picture of 

the general flow directions and discharge locations for the whole model domain. A total of 601 particles 

were released for the forward simulation.
25 

The forward simulated groundwater flowpaths are similar to the forward tracking paths Prych 

(1997) simulated, and indicate that most of the groundwater recharge from precipitation within the 

shipyard boundary discharges to the dry docks (fig. 7). Most of the recharge from precipitation that 

recharges on the western end of the shipyard discharges to dry docks 5 and 6, with the exception of the 

far western end where the flowpaths terminate in Puget Sound. There is also a small wedge between dry 

docks 5 and 6 where the flowpaths terminate in Puget Sound. Many of the particles that originate in the 

northwestern corner of the shipyard flow preferentially through a small valley that was filled in to the 

north of the main artificial fill area north of dry dock 6. The water-level altitudes in this filled valley are 

substantially lower than those in the surrounding native material on either side, leading the flowpaths 

through the filled valley before turning to the east and terminating in dry dock 5. Groundwater that 

recharges on the eastern end of the shipyard all discharges to dry docks 1, 3, and 4. Dry dock 4 draws 

water from either side as well as some from the far side of dry dock 2. Dry dock 2 was constructed 

without drains so no water is simulated to flow into it. The sheet-pile cutoff walls around dry docks 1 

and 3 exert a large influence on nearby flow paths. Dry dock 3 has more extensive sheet-pile cutoff 

walls that dry dock 1, causing groundwater that recharges to the east to bypass dry dock 3 and discharge 

into dry dock 1. 

For the backward simulation, particles were released at the end of the steady-state stress period 

at model cells containing each of 43 long-term monitoring wells, and MODPATH backtracked the 

particles to indicate where they entered the groundwater-flow system. Initial particle locations at each 

cell that contained one of the 43 long-term monitoring wells (fig. 8) were specified at the center of the 

cells and at the center of each of the 6 cell faces, for a total of 7 particles per cell. A total of 301 

particles were released for the backward simulation. The backward particle tracking (fig. 8) indicates 

that the most of the flowpaths that terminate at the long-term monitoring wells originate to the 

northwest of the shipyard, and that only a few wells intercept groundwater that originates as recharge 

within the shipyard boundary. Groundwater that originates farther north beyond the flowpath lines 

shown in figure 8 would likely discharge to the east in Puget Sound. 
26 

Figure 7. Map showing forward particle tracking from selected model cells within the shipyard for the groundwater flow model, Puget Sound Naval 

Shipyard, Naval Base Kitsap, Bremerton, Washington. 
27 

Figure 8. Map showing backward particle tracking from long-term monitoring wells for the groundwater flow model, Puget Sound Naval Shipyard, 

Naval Base Kitsap, Bremerton, Washington. 
28 

Summary 

Puget Sound Naval Shipyard is located on the northern shore of Sinclair Inlet in Puget Sound. A 

1997 multi-layer steady-state groundwater-flow model with homogeneous hydraulic characteristics was

updated with new interpretations of hydrogeologic unit presence and thickness, new recharge estimates

(from precipitation as well as inflow from the regional groundwater system—using General Head 

boundaries to determine the amount of regional groundwater inflow), new calibrated hydraulic 

parameter values, and increased vertical and areal resolution.

The shipyard and surrounding area overlies glacial and interglacial deposits and a substantial 

amount of fill along the shoreline to support terrestrial activities. Present in the model area are Vashon 

Till (Qvt), Vashon advance outwash (Qva), and seven older and deeper layers of alternately confining 

units and aquifer units. In the updated groundwater flow model, these are represented by 22 model 

layers and are calibrated such that each layer may have unique hydraulic characteristics. 

Annual precipitation of more than 56 inches results in recharge rates ranging between 0 and 

about 33 inches per year. Groundwater-flow directions reflect the regional pattern in the area—from 

topographic highs in the north and northwest generally south and southeast toward Puget Sound. Dry 

docks, with bottom altitudes ranging from -16.5 to -45.5 ft, are significant discharge locations.

The updated steady-state numerical (finite difference) groundwater model comprises 22 layers, 

104 rows, and 141 columns, with thinner layers at the top and narrower rows and columns at the 

locations of the dry docks. General head boundaries were used at the model perimeter except where 

horizontal flow barriers are used to represent bulkheads. The dry docks are represented by drain 

boundary cells. The bottom of the model is specified as a no-flow boundary. 

The updated model was calibrated using parameter estimation to average 2001–2005 water 

levels at monitoring wells within the shipyard. The final calibration had a mean residual value of +1.15 

ft. The flow directions and discharge locations predicted by this updated model generally match the 

1997 model despite refinements and other changes. 

Particle tracking using MODPATH was conducted in forward and backward tracking modes. 

For forward tracking, particles were assigned starting points at the water table for 4 percent (1 for every 

25 cells) of the active model cells within the shipyard and tracked to their final discharge locations. This 

allowed pathlines to be associated with specific drain boundary cells. For backward tracking, 7 particles 

per cell (center of all cells faces plus one centroid) were placed in 43 cells representing the screened 

intervals of long-term monitoring wells, and allowed to track backwards to the water table. This allowed 

each monitoring well to be associated with a recharge zone, and is intended to aid in evaluating the 

usefulness of the monitoring network with regard to specific source areas. 

In the updated model, most groundwater discharge recharged within the boundaries of the 

shipyard is to the dry docks; only at the western end of the shipyard does groundwater discharge directly 

to Puget Sound. Backward particle tracking for the existing long-term monitoring well network suggests 

that only a few wells intercept groundwater that originates as recharge within the shipyard boundary. 
29 

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32 

Table 3. Wells, measured water level altitudes, and model cell assignments used in calibration. 

[IRIMS is Installation Restoration Information Management System; water-level altitude in feet above NAVD88; see section 

“Hydrogeologic Units” for descriptions; FILL is artificial fill] 

Wells Name 

(IRIMS)

WA State Plane North, 

in feet

Water 

level

altitude

(ft)

Weight

Model Hydrogeologic 

unit

Northing Easting Layer Row Column

MW/SB 502-3

/ 

167-168 1191887 210163 11.15 4.5 4 49 20 Qva

MW/SB 502-2 169 1191897 210184 11.58 0.25 4 49 20 Qva

MW/SB 530-1 185 1190725 209037 10.42 0.25 4 63 14 Qva

GMW-2 207 1193817 209837 13.77 0.25 4 53 44 Qva

GMW-3 208A 1193892 209857 37.38 0.25 4 53 46 Qva

GMW-4 209A 1193889 209767 30.79 4.5 4 54 46 Qva

BACK-1 347 1192318 210684 12.73 4.5 5 44 23 Qva

MW377 377 1192656 209195 4.31 3 5 61 26 Qva

PS07-MW02 403 1196224 211093 2.92 4.5 5 39 94 Qva

BACK-2 431 1192730 210517 21.21 3 5 46 27 Qva

OUB-MW12 701 1196785 211368 4.87 10 5 38 109 Qva

PS03-MW02 202 1189722 207196 4.29 0.25 4 87 11 FILL

PS03-MW03 203 1189697 207020 6.27 4.5 4 89 10 FILL

MW204 204;243 1189284 206823 5.00 4.5 5 91 9 FILL

MW205 205 1189576 206942 3.49 0.25 5 89 10 FILL

GMW-1 206A 1193391 209640 -35.83 0.25 7 55 35 FILL

MW206 206B 1189842 207154 6.56 3 5 87 11 FILL

MW207 207;201 1189932 207449 5.77 1 5 84 11 FILL

MW-01 208B 1196964 209713 -31.29 0.25 8 53 114 QC1

MW208 208C 1189516 207324 8.39 4.5 4 86 10 FILL

MW-02 209B 1196983 209724 -31.37 0.25 8 53 115 QC1

GEW-11 216 1193489 209650 -33.74 0.25 6 55 36 FILL

GMWT-10 219;225 1193323 209738 -34.38 4.5 7 54 33 FILL

GMWT-14 223 1193381 209623 -35.01 4.5 7 56 34 FILL

GMWT-15 224 1193376 209473 -31.02 4.5 6 57 34 FILL

GMWT-17 226 1193636 209509 -31.97 4.5 7 57 40 FILL

MW238 238 1189060 206606 3.44 0.25 5 92 8 FILL

MW240 240;261 1188798 206432 5.96 4.5 5 93 7 FILL

MW241 241 1190207 207607 4.99 3 5 83 12 FILL

MW242 242;264 1189261 206986 6.21 1 5 89 9 FILL

GMWT-2 243;228 1193404 209730 -26.75 0.5 6 54 35 FILL

GMW-5 245 1193502 209680 -35.38 4.5 7 55 37 FILL

GMWT-7 247 1193522 209606 -34.53 4.5 7 56 37 FILL

MW-262 262;265 1189013 206777 6.71 1 5 91 8 FILL

MW-263 263 1188885 206527 6.74 0.25 4 93 8 FILL
33 

Wells Name 

(IRIMS)

WA State Plane North, 

in feet

Water 

level

altitude

(ft)

Weight

Model Hydrogeologic 

unit

Northing Easting Layer Row Column

MW-266 266 1189576 207221 6.15 10 4 87 10 FILL

MW-267 267 1190135 207887 10.10 0.25 5 79 12 FILL

PS12-MW01 301 1192138 208733 -2.57 3 5 67 22 FILL

PS12-MW02 302 1192120 208605 0.79 3 5 68 22 FILL

PS12-MW03 303 1192113 208412 3.08 4.5 5 71 22 FILL

PS10W-MW04 304 1192545 208446 -2.06 4.5 5 70 26 FILL

PS02-MW01 305 1191600 208316 1.53 4.5 5 72 19 FILL

PS02-MW04W 307 1191576 208758 2.69 3 5 67 19 FILL

PS02-MW03 308 1191714 208839 3.05 1 5 66 20 FILL

PS02-MW05 309;901 1191642 208212 1.87 1 5 74 19 FILL

MW310 310 1193221 208479 -29.69 1 7 69 32 FILL

MW-310R 310R 1193221 208473 -37.39 1 8 69 32 QC1

GMWT-9 311 1193489 209442 -35.28 1 7 58 36 FILL

MW312SHALO 312;385 1192579 208211 1.80 3 5 74 26 FILL

MW313 313 1191982 208219 3.29 4.5 5 74 21 FILL

MW316SHLLW 316 1192300 208963 -0.72 3 5 64 24 FILL

MW317 317 1193017 208733 -8.13 0.5 7 66 29 FILL

MW318 318 1192597 208829 -1.69 10 5 65 26 FILL

GMW-26 326 1193352 209404 -34.33 3 7 58 34 FILL

GMW-27 327 1193009 209539 -18.93 3 6 57 29 QC1

GMW-28 328 1193055 209390 0.95 4.5 6 58 30 QC1

MW417DEEP 350 1190740 209021 10.86 4.5 8 64 14 QC1

MW312DEEP 351 1192521 208219 -6.14 1 11 74 26 QC1

MW378 378 1192523 208862 -2.20 3 5 65 25 FILL

MW379 379 1192193 208880 -0.03 4.5 5 65 23 FILL

MW380 380 1193175 208269 -4.49 3 5 73 31 FILL

MW382 382 1193176 208850 -34.98 1 7 65 31 FILL

MW383 383 1191840 208294 2.59 0.25 5 73 20 FILL

MW386 386 1192516 208696 -3.14 3 5 67 25 FILL

MW388 388 1192321 208667 -2.23 4.5 5 67 24 FILL

MW389 389 1192433 208187 3.63 3 5 74 25 FILL

MW390 390 1192316 208337 0.61 1 5 72 24 FILL

MW391 391 1192521 208334 2.32 3 5 72 25 FILL

MW392 392 1192047 208191 7.96 3 5 74 22 FILL

MW392R 392R 1192035 208191 3.80 4.5 6 74 22 FILL

PS01-MW01 400 1194423 208366 6.70 3 4 70 53 FILL

PS01-MW02 401 1194196 208274 1.42 3 4 72 50 FILL

PS07-MW01 402 1196261 210843 -11.04 4.5 6 41 95 FILL

PS08-MW01A 404;752;756 1196912 209908 -16.14 1 6 51 112 FILL
34 

Wells Name 

(IRIMS)

WA State Plane North, 

in feet

Water 

level

altitude

(ft)

Weight

Model Hydrogeologic 

unit

Northing Easting Layer Row Column

PS08-MW01B 405 1196912 209914 -25.83 0.5 8 51 112 QC1

PS08-MW02A 406 1196818 209824 0.39 1 5 52 110 FILL

PS08MW02A- 406R 1196823 209829 4.63 3 6 52 111 FILL

PS08-MW02B 407 1196777 209830 -5.97 1 8 52 110 QC1

PS08-MW03A 408 1196733 209884 3.11 3 5 51 109 FILL

PS08-MW03B 409 1196732 209875 -9.63 1 8 51 109 QC1

PS09-MW01B 410 1193634 208425 -33.66 3 7 70 40 FILL

PS09- 410R 1193639 208430 -32.50 0.5 7 70 40 FILL

PS10E-MW01 411 1197550 209732 5.07 1 4 53 127 FILL

PS10C-MW01 412 1193993 208256 0.24 10 5 72 48 FILL

PS10C-MW02 413 1194762 209000 -11.68 4.5 6 62 59 FILL

PS10C-MW03 414 1195263 209650 -28.14 0.5 7 55 71 FILL

PS10C-MW04 415 1195326 209655 -35.70 4.5 7 54 72 FILL

PS10W-MW01 416 1190318 207860 5.33 3 5 80 13 FILL

PS10W-MW02 417;725 1190719 209020 10.66 4.5 4 64 14 FILL

PS10W-MW03 418 1191083 208021 5.41 3 5 77 16 FILL

RPW-1B 419 1190562 207831 3.48 3 5 80 14 FILL

RPW-2 420-1 1190618 207754 3.95 4.5 5 81 14 FILL

OUB-MW01 422 1197514 210420 4.52 3 5 45 126 FILL

OUB-MW02 423 1196763 210879 3.84 10 5 41 109 FILL

OUB-MW04 425 1195810 210732 -35.27 4.5 8 42 84 QC1

OUB-MW05 426 1195138 210110 -36.99 10 7 49 68 FILL

OUB-MW06 427 1194576 209227 -35.96 4.5 7 60 55 FILL

OUB-MW07 428R 1194171 209006 -32.19 0.5 7 63 50 FILL

OUB-MW09 430 1193484 208666 -32.66 4.5 7 67 37 FILL

PS07-MW03 432 1196141 210621 -22.36 4.5 6 43 92 FILL

PS07-MW04 433 1196429 210629 -4.51 4.5 7 43 99 FILL

PS11-MW03C 670 1193516 209767 -38.91 4.5 7 54 37 FILL

PS11-MW05 672 1193445 209474 -30.69 0.5 7 57 36 FILL

OUB-MW13 702 1197903 210163 4.82 3 5 48 130 FILL

OUB-MW14 703 1197165 210576 0.25 10 5 44 119 FILL

OUB-MW15 704 1196900 210619 3.24 4.5 5 43 112 FILL

OUB-MW17 706 1195895 210920 -37.07 3 7 41 85 FILL

OUB MW18 707 1195442 210612 -37.95 4.5 8 44 75 QC1

OUB-MW23 709 1194430 208370 3.81 3 5 70 54 FILL

OUB-MW19 710 1194238 208484 -2.54 10 5 69 51 FILL

OUB-MW-20 713 1193837 208161 3.40 3 5 74 45 FILL

OUB-MW21 714 1193869 208763 -31.62 1 7 66 46 FILL

OUB-MW24 715R 1191146 207759 3.53 3 5 81 16 FILL
35 

Wells Name 

(IRIMS)

WA State Plane North, 

in feet

Water 

level

altitude

(ft)

Weight

Model Hydrogeologic 

unit

Northing Easting Layer Row Column

OUB-MW22 716A 1196917 210286 -9.02 3 5 47 112 FILL

GMWT-20 716B 1193214 209614 -33.12 4.5 6 56 31 FILL

GMWT-19 717 1193262 209669 -32.92 3 7 55 32 FILL

GMWT-18 718A 1193336 209509 -35.69 3 7 57 33 FILL

OUB-MW-25 718B 1191312 208310 5.22 4.5 5 73 17 FILL

LTMP-1 720_w 1190425 207686 4.07 3 5 82 13 FILL

LTMP-2 721 1190840 207693 4.59 4.5 5 81 15 FILL

LTMP-3 722 1191357 208197 3.22 3 5 75 17 FILL

LTMP-4 723 1195016 210016 -38.18 3 7 50 65 FILL

LTMP-5 724_w 1197729 209759 4.18 3 4 52 129 FILL

GMWT-22 735 1193370 209203 -16.38 3 6 60 34 FILL

GMWT-23 736 1193474 209180 -34.44 3 7 61 36 FILL

GMWT-24 737 1193707 209050 -34.61 3 7 62 42 FILL

GMWT-25 738 1193478 208965 -34.92 3 7 63 37 FILL

GMWT-26 750 1193464 209173 -56.82 4.5 8 61 36 QC1

PS08-MW07 753 1196917 209986 -17.52 1 6 50 113 FILL

MONITOR 801-2 1190726 208324 8.30 3 4 73 14 FILL

MONITOR 803 1190896 208335 7.63 0.25 4 73 15 FILL

MONITOR 804 1190734 208239 7.51 0.25 4 74 14 FILL

MONITOR 805 1190865 208233 7.25 0.25 5 74 15 FILL

MONITOR 806 1190935 208211 6.54 0.25 4 75 15 FILL

MONITOR 807 1191068 208317 5.82 0.25 5 73 16 FILL

MONITOR 808 1191173 208169 -3.86 0.25 5 75 16 FILL

MONITOR 809 1190896 208346 8.19 4.5 5 72 15 FILL

MONITOR 810 1191003 208277 6.89 3 5 73 15 FILL

MONITOR 811 1190889 208460 9.44 3 4 70 15 FILL

MW900 900 1191525 208548 3.83 1 5 69 18 FILL

MW902 902 1191927 209154 5.21 3 5 61 21 QC1

MW903 903 1197815 210203 4.96 4.5 5 47 129 FILL

MW904 904 1196152 210879 3.29 4.5 5 41 92 FILL

MW905 905 1195894 210990 -37.20 4.5 8 40 85 QC1

MW907 907 1195523 210740 -36.51 10 8 42 77 QC1

PS11-MW01L 346 1193695 210817 7.06 3 13 42 40 QA1

MW316DEEP 352 1192305 208963 -0.96 3 13 64 24 QA1

OUB-MW03 424 1196761 210871 -1.03 10 13 41 109 QA1

OUB-MW08 429 1194169 209000 -31.65 3 14 63 50 QA1

OUB-MW-16 705 1196264 210838 5.78 4.5 14 41 95 QA1

MW-268 268 1189574 206936 11.27 0.25 16 90 10 QC2

MW381 381 1192229 208227 4.90 1 15 74 23 QC2

Publishing support provided by the U.S. Geological Survey

Science Publishing Network, Tacoma Publishing Service Center

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

 Director, Washington Water Science Center

U.S. Geological Survey

934 Broadway, Suite 300

Tacoma, Washington 98402 

http://wa.water.usgs.gov
Jones and others—Numerical Simulation of Groundwater Flow at Puget Sound Naval Shipyard, Naval Base Kitsap, Bremerton, Washington—Open-File Report 2016–1135

ISSN 2331-1258 (online)

http://dx.doi.org/10.3133/ofr20161135