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Geohydrological Characterization, Water-Chemistry, and Ground-Water Flow Simulation Model of the Sonoma Valley Area, Sonoma County, California

By Christopher D. Farrar, Loren F. Metzger, Tracy Nishikawa, Kathryn M. Koczot, and Eric G. Reichard


With a section on Basement Rock Configuration Interpreted from Gravity Data

By Victoria E. Langenheim



Scientific Investigations Report 2006-5092

Sacramento, California 2006

In cooperation with the Sonoma County Water Agency

Complete accessible text of report (15.1 MB PDF)

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The Sonoma Valley, located about 30 miles north of San Francisco, is one of several basins in Sonoma County that use a combination of ground water and water delivered from the Russian River for supply. Over the past 30 years, Sonoma Valley has experienced rapid population growth and land-use changes. In particular, there has been a significant increase in irrigated agriculture, predominantly vineyards. To provide a better understanding of the ground-water/surface-water system in Sonoma Valley, the U.S. Geological Survey compiled and evaluated existing data, collected and analyzed new data, and developed a ground-water flow model to better understand and manage the ground-water system. The new data collected include subsurface lithology, gravity measurements, groundwater levels, streamflow gains and losses, temperature, water chemistry, and stable isotopes.

Sonoma Valley is drained by Sonoma Creek, which discharges into San Pablo Bay. The long-term average annual volume of precipitation in the watershed is estimated to be 269,000 acre-feet. Recharge to the ground-water system is primarily from direct precipitation and Sonoma Creek. Discharge from the ground-water system is predominantly outflow to Sonoma Creek, pumpage, and outflow to marshlands and to San Pablo Bay. Geologic units of most importance for groundwater supply are the Quaternary alluvial deposits, the Glen Ellen Formation, the Huichica Formation, and the Sonoma Volcanics. In this report, the ground-water system is divided into three depth-based geohydrologic units: upper (less than 200 feet below land surface), middle (between 200 and 500 feet), and lower (greater than 500 feet).

Synoptic streamflow measurements were made along Sonoma Creek and indicate those reaches with statistically significant gains or losses. Changes in ground-water levels in wells were analyzed by comparing historical contour maps with the contour map for 2003. In addition, individual hydrographs were evaluated to assess temporal changes by region. In recent years, pumping depressions have developed southeast of Sonoma and southwest of El Verano.

Water-chemistry data for samples collected from 75 wells during 200204 indicate that the ground-water quality in the study area generally is acceptable for potable use. The water from some wells, however, contains one or more constituents in excess of the recommended standards for drinking water. The chemical composition of water from creeks, springs, and wells sampled for major ions plot within three groups on a trilinear diagram: mixed-bicarbonate, sodium-mixed anion, and sodium-bicarbonate. An area of saline ground water in the southern part of the Sonoma Valley appears to have shifted since the late 1940s and early 1950s, expanding in one area, but receding in another. Sparse temperature data from wells southwest of the known occurrence of thermal water suggest that thermal water may be present beneath a larger part of the valley than previously thought. Thermal water contains higher concentrations of dissolved minerals than nonthermal waters because mineral solubilities generally increase with temperature. Geohydrologic Characterization, Water-Chemistry, and Ground-Water Flow Simulation Model of the Sonoma Valley Area, Sonoma County, California

Oxygen-18 (δ18Ο) and deuterium (δD) values for water from most wells plot along the global meteoric water line, indicating that recharge primarily is derived from the direct infiltration of precipitation or the infiltration of seepage from creeks. Samples from shallow- and intermediate-depth wells located near Sonoma Creek and (or) in the vicinity of Shellville plot to the right of the global meteoric water line, indicating that these waters are partly evaporated. The δ18Ο and δD composition of water from sampled wells indicates that water from wells deeper than 200 feet is isotopically lighter (more negative) than water from wells less than 200 feet deep, possibly indicating that older ground water was recharged under cooler and (or) wetter climatic conditions. Alternatively, isotopically lighter water could represent recharge originating from higher elevations of the Sonoma Creek watershed.

A simulation model of ground-water flow in the Sonoma Valley was developed using MODFLOW-2000. The eightlayer model was parameterized to represent the three geohydrologic units. Model development required estimating model fluxes (pumpage and recharge) and hydraulic parameters (hydraulic conductivity and storage) for the area. The hydraulic barrier created by the Eastside Fault was incorporated into the model. In general, the calibrated model simulated waterlevel declines that matched measured values. The cumulative volume of water pumped from the ground-water basin between 1975 and 2000 was about 1.97 105 acre-ft; of this total pumpage, the model simulated that about 9 percent (1.73 104 acre-ft) was removed from storage. This fairly small decrease in storage explains the localized nature of the water-level declines. A sensitivity analysis indicated that the model would most benefit from additional data collection in the northern part of the basin.




Location of the Study Area

Purpose and Scope

Land and Water Use


Previous Investigations and Databases


Physiography and Geologic Setting


Basement Rocks

Basin Fill

Tertiary Sedimentary Rocks

Sonoma Volcanics

Huichica Formation

Glen Ellen Formation

Quaternary Alluvial Units

Bay Mud Deposits

Geologic Structure


Surface-Water Hydrology

Ground-Water Hydrology

Water-Bearing Properties

Effects of Geologic Structures on Ground-Water Movement



Streamflow Gains and Losses

Methods of Data Collection and Analysis

Streamflow Measurements and Estimated Gains and Losses

Watershed Hydrologic Budget

Ground-Water Levels and Movement

Comparison of Water-Level Contour Maps: 1950, 1980, and 2003

Long-Term Changes in Ground-Water Levels in Different Parts of the Sonoma Valley

Surface-Water and Ground-Water Chemistry

Methods of Water Sampling and Analysis

General Chemical Composition of Surface, Spring, and Ground Water

Constituents of Potential Concern

High-Salinity Waters

Ground-Water Temperature

Chemical Composition of Thermal Waters

Oxygen-18 and Deuterium


Stable Isotope Results

Ground-Water Flow Model

Model Discretization

Spatial Discretization

Temporal Discretization

Model Boundaries

Subsurface Properties

Hydraulic Conductivity

Storage Coefficient and Specific Yield


Stream-Aquifer Interactions

Model Inflow

Model Outflow

Model Calibration

Simulated Hydraulic Heads

Areal Distribution: Steady State and 2000

Simulated Hydrographs

Simulated Water Budget

Model Fit

Streamflow Gains and Losses

Sensitivity Analysis

Uses and Limitations of the Ground-Water Flow Model


References Cited


Appendix A. Basement Rock Configuration Interpreted from Gravity Data

Appendix B. Water Levels at Selected Wells in the Sonoma Valley

Appendix C. Construction data, and spring 2003 water levels for selected wells used for geologic cross sections, water-level monitoring, chemistry sampling, and temperature logging in the Sonoma Valley, Sonoma County, California

Appendix D. Field measurements and laboratory analyses of samples from streamflow-measurement stations, springs, and ground-water wells, Sonoma Valley, Sonoma County, California, 2002–04

Appendix E. Summary of specific conductance and temperature measurements in samples from springs, ground-water wells, and miscellaneous sources, Sonoma Valley, Sonoma County, California, 1969–2004

Appendix F. Summary of delta deuterium and delta oxygen-18 values in samples from streamflow-measurement stations, springs, ground-water wells, and miscellaneous sources, Sonoma Valley, Sonoma County,California, 2002–04

Appendix G. Methodology for Estimating Pumpage for the Ground-Water Simulation Model

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