River-Aquifer Interactions, Geologic Heterogeneity, and Low-Flow Management

U.S. Geological Survey (USGS) | ?

Low river flows are commonly controlled by river-aquifer exchange, the magnitude of which is governed by hydraulic properties of both aquifer and aquitard mater

Low river flows are commonly controlled by river-aquifer exchange, the magnitude of which is governed by hydraulic properties of both aquifer and aquitard materials beneath the river. Low flows are often important ecologically. Numerical simulations were used to assess how textural heterogeneity of an alluvial system influences river seepage and low flows. The Cosumnes River in California was used as a test case. Declining fall flows in the Cosumnes River have threatened Chinook salmon runs. A ground water–surface water model for the lower river basin was developed, which incorporates detailed geostatistical simulations of aquifer heterogeneity. Six different realizations of heterogeneity and a homogenous model were run for a 3-year period. Net annual seepage from the river was found to be similar among the models. However, spatial distribution of seepage along the channel, water table configuration and the level of local connection, and disconnection between the river and aquifer showed strong variations among the different heterogeneous models. Most importantly, the heterogeneous models suggest that river seepage losses can be reduced by local reconnections, even when the regional water table remains well below the riverbed. The percentage of river channel responsible for 50% of total river seepage ranged from 10% to 26% in the heterogeneous models as opposed to 23% in the homogeneous model. Differences in seepage between the models resulted in up to 13 d difference in the number of days the river was open for salmon migration during the critical fall months in one given year.

Rivers that Depend on Aquifers: Drafting SGMA Groundwater Plans with Fisheries in Mind

Golden Gate University (GSU) | April 12th, 2018

In California, surface waters have historically been regulated as if they were unconnected to groundwater. Yet, in reality, surface waters and groundwater are often hydro

In California, surface waters have historically been regulated as if they were unconnected to groundwater. Yet, in reality, surface waters and groundwater are often hydrologically connected. Many of the rivers that support fisheries such as salmon and trout are hydrologically dependent on tributary groundwater to maintain instream flow. This means that when there is intensive pumping of tributary groundwater the result can be reductions in instream flow and damage to fisheries. For this reason, stakeholders concerned about adequate instream flows for fisheries in California’s rivers, streams and creeks need to be effectively engaged in the implementation of California’s Sustainable Groundwater Management Act (SGMA). Consider the Scott River in Northern California, part of the larger Klamath River Basin. Nearby groundwater contributes to the Scott River. When high volumes of groundwater are extracted from nearby wells, it depletes the Scott River’s instream flow with adverse impacts on salmon and steelhead trout. As discussed further in Section VI of this guidebook, this has led to litigation over the application of California public trust law to groundwater extraction affecting Scott River instream flows, and efforts to use SGMA to ensure that groundwater pumping near the Scott River is compatible with the instream flow needs of fisheries. Situations similar to the Scott River surface and groundwater basin are unfolding throughout California. On a statewide basis, how pervasive is the effect of groundwater pumping on surface water flows? Research by Maurice Hall of the Environmental Defense Fund, utilizing the California Department of Water Resources Central Valley Groundwater Surface Flow Model, provides us with some sense of the magnitude of the problem. In a May 2018 presentation, Hall reported: What the model showed us is that early in the 1900s, 1940s and 1950s, the Sacramento River received a net inflow from the groundwater of something like 1 million acre feet a year…Since that time, the groundwater levels have gone down, and the amount of water that has flowed into the Sacramento River from the surrounding groundwater has gone down accordingly to the point that when we were doing this modeling around 2010, it appeared that on average, the Sacramento River lost just about as much as it gained from the surrounding groundwater in the valley floor. This is the Sacramento River and all of its tributaries upstream of the Sacramento…So the net effect over that period is there was roughly on average 900,000 acre-feet per year less water showing up in the  Sacramento River at Sacramento.” (Hall and O’Brien). SGMA was enacted in 2014. Pursuant to SGMA, by June 2017 a groundwater sustainability agency was required to be designated for each groundwater basin in California. Each groundwater sustainability agency in high and medium priority basins must prepare and adopt a Groundwater Sustainability Plan (SGMA Groundwater Plan) by 2020 if the basin is deemed to be in a critical state of overdraft or 2022 for all remaining high and medium priority basins. Each SGMA Groundwater Plan must detail how the groundwater basin will be managed to avoid overdraft conditions and, importantly for fisheries, to avoid adverse impacts on hydrologically connected surface waters. Although groundwater sustainability agencies and fishery stakeholders recognize that the groundwater-surface water connection needs to be addressed in SGMA Groundwater Plans, at present there is limited guidance on how to do this. That is, what are the specific types of information, modeling, monitoring, and pumping provisions that should be included in SGMA Groundwater Plans to ensure that groundwater extraction does not cause significant adverse impacts on fisheries? The purpose of this guidebook is to provide such guidance.

Salt and Nutrient Management Plan Santa Clara River Valley East Subbasin

California State Water Resources Control Board (SWRCB) | October 25th, 2016

In accordance with the State Water Resources Control Board’s (SWRCB’s) Recycled Water Policy, the Upper Santa Clara River Integrated Regional Water Management Group

In accordance with the State Water Resources Control Board’s (SWRCB’s) Recycled Water Policy, the Upper Santa Clara River Integrated Regional Water Management Group (IRWMG), which is comprised of Castaic Lake Water Agency (CLWA), City of Santa Clarita, CLWA Santa Clarita Water Division (SCWD), Los Angeles County Flood Control District (LACFCD), Newhall County Water District (NCWD), San Gabriel & Lower Los Angeles Rivers and Mountains Conservancy, Santa Clarita Valley Sanitation District (SCVSD) and Valencia Water Company (VWC), have entered into a Memorandum of Understanding (MOU) to prepare a Salt and Nutrient Management Plan (SNMP) for the Santa Clara River Valley East Groundwater Subbasin (East Subbasin). This group of agencies, collectively known as the SNMP Task Force (Task Force) and facilitated by the CLWA, have directed the preparation of this SNMP, which was prepared using guidance set forth by the Los Angeles Regional Water Quality Control Board (LARWQCB). The purpose of this SNMP is to determine the current (ambient) water quality conditions in the East Subbasin and to ensure that all water management practices, including the use of recycled water, are consistent with water quality objectives. This SNMP is intended to provide the framework for water management practices to ensure protection of beneficial uses, and allow for the sustainability of groundwater resources consistent with the Water Quality Control Plan Los Angeles Region (Basin Plan). Additionally, compliance with the California Environmental Quality Act (CEQA) and approval by LARWQCB staff is required. As part of the SNMP, a monitoring plan has been developed for the East Subbasin which identifies key monitoring locations within each subunit for both surface water and groundwater.

Scott River Ajudication Decree

California State Water Resources Control Board (SWRCB) | January 30th, 1980

The water rights set forth in this decree consist of (1) all surface water rights in the Scott River stream system, as defined in paragraph 2, excluding springs or standi

The water rights set forth in this decree consist of (1) all surface water rights in the Scott River stream system, as defined in paragraph 2, excluding springs or standing pools not specifically included in this decree which do not contribute to a flowing stream or have no natural outlet, and excluding water which naturally sustains mountain meadows and other native vegetation without artificial diversion from a flowing stream; (2) all rights to supporting underflow and (3) all rights to ground water that i s interconnected with tlie Scott River as delineated on the State Water Resources Control Board map, hereinafter referred to as the SWRCB map, and as defined in Paragraph 4.

Scott Valley Integrated Hydrologic Model: Data Collection, Analysis, and Water Budget Final Report

University of California, Davis (UC Davis) | November 14th, 2017

The Scott Valley is an agricultural groundwater basin in Northern California, within the Scott River watershed and part of the much larger Klamath Basin watershed straddl

The Scott Valley is an agricultural groundwater basin in Northern California, within the Scott River watershed and part of the much larger Klamath Basin watershed straddling the California-Oregon border. The Scott River provides important habitat for salmonid fish, including spawning and rearing habitat for coho and fall-run Chinook salmon and steelhead trout. Sufficient flows at adequately low temperatures during summer, for rearing, and fall, for spawning, are critical for healthy fish habitat in the mainstem and tributaries. This report presents the data assembled and the methods used for data analysis and data modeling to prepare the Scott Valley Integrated Hydrologic Model Version 2, which is currently under development. The report includes precipitation data analysis, streamflow data analysis and modeling, geology and groundwater data review and analysis, evapotranspiration and soils data analysis, and preparation of relevant watershed, land use, topography, and irrigation data. The data collection and analysis efforts culminate in the development of a spatio-temporally distributed soil water budget model for the Scott Valley. The soil water budget model is used to determine spatially and temporally varying groundwater pumping rates, surface water diversion rates, and groundwater recharge across the groundwater basin. The spatial resolution of the soil water budget model is by individual fields (land use polygons). Temporal discretization is in daily time steps for the period from October 1, 1990 to September 30, 2011. This period includes several dry years, average years, and wet year periods. Methods and results of the soil water budget model are presented in this report. This report represents the next step toward a better understanding of the interactions between groundwater, surface water, land-use, and agricultural practices with a specific focus on the seasonal impacts of groundwater pumping on streamflow during critical low flow periods. The work presented here relies on an extensive data collection facilitated by the voluntary and active collaboration of communities, landowners, the Scott River Watershed Council (SRWC), the Siskiyou Resource Conservation District (SRCD), and the Scott Valley Groundwater Advisory Committee (GWAC) which has been appointed by the Board of Supervisors in January 2011, meeting monthly since April 2011 and advising UC Davis on its data collection and modeling efforts. In the data analysis and during the model development, numerous assumptions have been made as is common in building a conceptual and numerical integrated hydrologic model. Models cannot represent the complexity of the real system, but are an effort to capture salient hydrologic features with sufficient accuracy to develop modeling results that are useful for a better understanding of the watershed dynamics and water balance.

Simulated Effects of Future Water Availability and Protected Species Habitat in a Perennial Wetland, Santa Barbara County, California

Water (MDPI) | April 21st, 2025

This study evaluates the potential water availability in Barka Slough and the effects of changing hydrological conditions on the aquatic habitat of five protected species

This study evaluates the potential water availability in Barka Slough and the effects of changing hydrological conditions on the aquatic habitat of five protected species.

Simulating the sensitivity of evapotranspiration and streamflow to large-scale groundwater depletion

American Association for the Advancement of Science (AAAS) | June 19th, 2019

Groundwater pumping has caused marked aquifer storage declines over the past century. In addition to threatening the viability of groundwater-dependent economic activitie

Groundwater pumping has caused marked aquifer storage declines over the past century. In addition to threatening the viability of groundwater-dependent economic activities, storage losses reshape the hydrologic landscape, shifting groundwater surface water exchanges and surface water availability. A more comprehensive understanding of modern groundwater-depleted systems is needed as we strive for improved simulations and more efficient water resources management. Here, we begin to address this gap by evaluating the impact of 100 years of groundwater declines across the continental United States on simulated watershed behavior. Subsurface storage losses reverberate throughout hydrologic systems, decreasing streamflow and evapotranspiration. Evapotranspiration declines are focused in water-limited periods and shallow groundwater regions. Streamflow losses are widespread and intensify along drainage networks, often occurring far from the point of groundwater abstraction. Our integrated approach illustrates the sensitivity of land surface simulations to groundwater storage levels and a path toward evaluating these connections in large-scale models.

Simulation of Ground-Water / Surface-Water Flow in the Santa Clara–Calleguas Ground-Water Basin, Ventura County, California

U.S. Geological Survey (USGS) | July 17th, 2003

Ground water is the main source of water in the Santa Clara–Calleguas ground-water basin that covers about 310 square miles in Ventura County, California. A steady incr

Ground water is the main source of water in the Santa Clara–Calleguas ground-water basin that covers about 310 square miles in Ventura County, California. A steady increase in the demand for surface- and ground-water resources since the late 1800s has resulted in streamflow depletion and ground-water overdraft. This steady increase in water use has resulted in seawater intrusion, inter-aquifer flow, land subsidence, and ground-water contamination.  The Santa Clara–Calleguas Basin consists of multiple aquifers that are grouped into upper- and lower-aquifer systems. The upper-aquifer system includes the Shallow, Oxnard, and Mugu aquifers. The lower-aquifer system includes the upper and lower Hueneme, Fox Canyon, and Grimes Canyon aquifers. The layered aquifer systems are each bounded below by regional unconformities that are overlain by extensive basal coarse-grained layers that are the major pathways for ground-water production from wells and related seawater intrusion. The aquifer systems are bounded below and along mountain fronts by consolidated bedrock that forms a relatively impermeable boundary to ground-water flow. Numerous faults act as additional exterior and interior boundaries to ground-water flow. The aquifer systems extend offshore where they crop out along the edge of the submarine shelf and within the coastal submarine canyons. Submarine canyons have dissected these regional aquifers, providing a hydraulic connection to the ocean through the submarine outcrops of the aquifer systems. Coastal landward flow (seawater intrusion) occurs within both the upper- and lower-aquifer systems. A numerical ground-water flow model of the Santa Clara–Calleguas Basin was developed by the U.S. Geological Survey to better define the geohydrologic framework of the regional ground-water flow system and to help analyze the major problems affecting water-resources management of a typical coastal aquifer system. Construction of the Santa Clara–Calleguas Basin model required the compilation of geographic, geologic, and hydrologic data and estimation of hydraulic properties and flows. The model was calibrated to historical surface-water and ground-water flow for the period 1891–1993. Sources of water to the regional ground-water flow system are natural and artificial recharge, coastal landward flow from the ocean (seawater intrusion), storage in the coarse-grained beds, and water from compaction of fine-grained beds (aquitards). Inflows used in the regional flow model simulation include streamflows routed through the major rivers and tributaries; infiltration of mountain-front runoff and infiltration of precipitation on bedrock outcrops and on valley floors; and artificial ground-water recharge of diverted streamflow, irrigation return flow, and treated sewage effluent.  Most natural recharge occurs through infiltration (losses) of streamflow within the major rivers and tributaries and the numerous arroyos that drain the mountain fronts of the basin. Total simulated natural recharge was about 114,100 acre-feet per year (acre-ft/yr) for 1984–93: 27,800 acre-ft/yr of mountain-front and bedrock recharge, 24,100 acre-ft/yr of valley-floor recharge, and 62,200 acre-ft/yr of net streamflow recharge. Artificial recharge (spreading of diverted streamflow, irrigation return, and sewage effluent) is a major source of ground-water replenishment. During the 1984–93 simulation period, the average rate of artificial recharge at the spreading grounds was about 54,400 acre-ft/yr, 13 percent less than the simulated natural recharge rate for streamflow infiltration within the major rivers and tributaries. Estimated recharge from infiltration of irrigation return flow on the valley floors averaged about 51,000 acre-ft/yr, and treated sewage effluent averaged about 9,000 acre-ft/yr. Artificial recharge as streamflow diversion to the spreading grounds has occurred since 1929, and treated-sewage effluent has been discharged to stream channels since 1930.  Under predevelopment conditions, the largest discharge from the ground-water system was outflow as coastal seaward flow and evapotranspiration. Pumpage of ground water from thousands of water-supply wells has diminished these outflows and is now the largest outflow from the ground-water flow system. The distribution of pumpage for 1984–93 indicates that most of the pumpage occurs in the Oxnard Plain subareas (37 percent) and in the upper Santa Clara River Valley subareas (37 percent). The total average simulated pumpage was about 247,000 acre-ft/yr (59 percent); of which about 146,000 acre-ft/yr was from the Fox Canyon Groundwater Management Agency (FGMA) subareas and 101,000 acre-ft/yr (41 percent) from the non-FGMA subareas. Of the total 1984–93 pumpage, 46 percent was contributed by natural recharge, 22 percent was contributed by artificial recharge from diverted streamflow, 20 percent was contributed by irrigation return flow, 4 percent was contributed from sewage-effluent infiltration, 6 percent was contributed from storage depletion, and 2 percent was contributed from coastal landward flow (seawater intrusion). Seawater intrusion was first suspected in 1931 when water levels were below sea level in a large part of the Oxnard Plain. The simulation of regional ground-water flow indicated that coastal landward flow (seawater intrusion) began in 1927 and continued to the end of the period of simulation (1993). During wet periods or periods of reduced demand for ground water, the direction of coastal flow in the upper-aquifer system reverses from landward to seaward. During the 1984–93 period, the simulated total net seaward flow was 9,500 acre-feet in the upper-aquifer system, which is considerably less than that simulated for predevelopment conditions. During the same period, total simulated landward flow in the lower-aquifer system was 64,200 acre-feet. Water-level declines in the basin have induced land subsidence that was first measured in 1939 and have resulted in as much as 2.7 feet land subsidence in the southern part of the Oxnard Plain. The model simulated a total of 3 feet of land subsidence in the southern part of the Oxnard Plain and as much as 5 feet in the Las Posas Valley subbasins. Model simulations indicate that most of the land subsidence occurred after the drought of the late 1920s and during the agricultural expansion of the 1950s and 1960s. The results also indicate that subsidence occurred primarily in the upper-aquifer system prior to 1959, but in the lower-aquifer system between 1959–93 owing to an increase in pumpage from the lower-aquifer system. The calibrated ground-water flow model was used to assess future ground-water conditions based on proposed water-supply projects in the existing management plan for the Santa Clara–Calleguas ground-water basin. All the projections of the proposed water-supply projects in the existing management plan have reduced pumpage in the FGMA areas which resulted in a reduction but not an elimination of storage depletion and related coastal landward flow (seawater intrusion) and subsidence, a reduction in streamflow recharge, and an increase in coastal seaward flow and underflow to adjacent subareas from the Oxnard Plain. A comparison of management simulations based on historical inflows and a spectral estimate of inflows shows increased coastal landward flow (seawater intrusion), storage depletion, and increased land subsidence due to a drought projected earlier in the spectral estimate of inflows than in the historical inflows. The spectral estimate probably provides a smoother and more realistic transition between historical and future climatic conditions. The model also was used to simulate potential alternative water-supply projects in the Santa Clara–Calleguas ground-water basin. These seven alternative water-supply projects were proposed to help manage the effects of increasing demand and variable supply on seawater intrusion, subsidence, increased withdrawal from storage, and vertical and lateral flow between subareas and aquifers systems. Stopping pumpage primarily in the lower-aquifer system in the South Oxnard Plain subarea had the largest effect on reducing coastal landward flow (seawater intrusion) of all the potential cases evaluated. Shifting pumpage from the lower- to the upper-aquifer system in the South Oxnard Plain subarea yielded the largest combined effect on coastal flow with a reduction of coastal landward flow in the lower-aquifer system and coastal seaward flow from the upper-aquifer system. A seawater-barrier injection project stopped coastal landward flow (seawater intrusion) in the upper-aquifer system but also resulted in large quantities of coastal seaward flow. The recharge of water in Happy Camp Canyon resulted in water-level rises that were above land surface (not feasible) in the East Las Posas Valley subarea but in no significant changes in hydrologic conditions in other parts of the basin. 

Simulation of Ground-water Flow in the Mojave River Basin, California

U.S. Geological Survey (USGS) | July 1st, 2001

Simulation of Ground-Water/Surface-Water Flow in the Santa Clara–Calleguas Ground-Water Basin, Ventura County, California

U.S. Geological Survey (USGS) | July 15th, 2003

Ground-water is the main source of water in the Santa Clara–Calleguas ground-water basin that covers about 310 square miles in Ventura County, California. A steady incr

Ground-water is the main source of water in the Santa Clara–Calleguas ground-water basin that covers about 310 square miles in Ventura County, California. A steady increase in the demand for surface- and ground-water resources since the late 1800s has resulted in streamflow depletion and ground-water overdraft. This steady increase in water use has resulted in seawater intrusion, inter-aquifer flow, land subsidence, and ground-water contamination.