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Scientific Investigations Report 2007–5216

Scientific Investigations Report 2007–5216

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Hydrologists traditionally regarded streams and ground water as distinct, independent resources to be utilized and managed separately. However, with increased demands on water supplies, hydrologists realized that streams and ground water are parts of a single, interconnected resource (Winter and others, 1998). Attempts to distinguish these resources for analytical or regulatory purposes often meet with difficulty because sustained depletions of one resource negatively impact the other. An understanding of the interconnections between surface water and ground water is therefore essential. Scientists have begun to show that local hydrologic interactions between surface water and ground water play an important role in stream ecosystem structure and function (Gilbert and others, 1994; Findlay, 1995; Brunke and Gonser, 1997). Water that passes back and forth between the surface water and subsurface water influences the fate and mobilization of trace metals and organic pollutants, and can enhance biogeochemical reactions that can affect downstream water quality. Understanding these interactions at small scales requires knowledge of ground-water flowpaths and their linkages to streams, rates of exchange between stream and ground-water systems, and the mechanisms that generate spatial (channel unit, reach, and watershed) and temporal (diel, seasonal) variations in these processes (Wroblicky and others, 1998). Rates of exchange across a streambed are most commonly estimated using one or more of the following approaches: (1) Darcy water-flux calculations, (2) tracer-based approaches, and (3) direct measurements across a streambed using a device such as a seepage meter. The Darcy approach calculates water fluxes across streambeds on the basis of two-dimensional maps of hydraulic head, estimates of hydraulic conductivity of near-channel sediment, and the basic governing equations for ground-water flow (Harvey and Wagner, 2000). The tracer approach lets one observe an introduced tracer (for example, salt, deionized water, or bromide) or an environmental tracer (temperature or specific conductance) to infer flux rates across the streambed. A seepage meter directly measures vertical flux across the sediment–water interface.


The Merced River, located in the San Joaquin River Basin in central California, was chosen by the U.S. Geological Survey’s (USGS) National Water-Quality Assessment (NAWQA) Program as one of five study areas in a national study of how hydrological processes and agricultural practices interact to affect the transport and fate of agricultural chemicals in nationally important agricultural settings. The key to achieving this objective is an understanding of how the agricultural chemicals move through each hydrologic compartment, as well as estimating rates of exchange between compartments. Five hydrologic compartments were monitored: the atmosphere, surface water, the unsaturated zone, ground water, and the hyporheic zone (surface-water–ground-water, or sw–gw, interaction). This project focused on estimating rates of exchange between the surface water and ground water across the sediment–water interface in the lower Merced River, California.

Estimates of ground-water seepage were made along a 100-m reach in the lower Merced River. The site location was chosen on the basis of reconnaissance work. The criteria required that the reach be gaining, easily accessible, and located next to agricultural land on which agricultural chemicals of interest were being applied. The location of the reach also bracketed the end of the ground-water flowpath compartment and was near the atmosphere and unsaturated zone compartment in the adjacent almond orchard.

Purpose and Scope

This report provides information regarding the use of seepage meters in a river environment and the application of temperature as a tracer in the shallow riverbed subsurface to predict rates of exchange using a USGS heat and flow model. Vertical estimates of ground-water seepage rates through a 100-m reach of the Merced River, California, are presented. Seepage rates were estimated directly using seepage meters, and indirectly using temperature and head measurements to calibrate a flow and heat transport model, VS2DH. Indirect seepage rates were constrained by hydraulic conductivity estimates from sieve analysis of streambed sediments and slug tests.

Study Area

The study area is located in the lower Merced River Basin, which lies on the east side of the San Joaquin Valley in the San Joaquin Basin and is approximately 831 km2 (fig.1). Two transects across a 100-m reach were equipped with monitoring wells that recorded continuous temperature and pressure head throughout the study period (fig. 2 and table 1). Table 1 describes the location and type of monitoring equipment depicted in figure 2. The lower Merced River Basin setting is predominately agriculture on the valley floor and lies within the flat structural basin of the San Joaquin Valley. The upstream part of the lower basin extends eastward into the lower foothills of the Sierra Nevada. The San Joaquin Valley is bounded by the Sierra Nevada to the east, the Coast Ranges to the west, the Tehachapi Mountains to the south, and the Sacramento–San Joaquin Delta to the north. The boundary of the basin is defined by the topographic drainage divides and in some areas, by canals and laterals that serve this area. The altitude ranges from 22 m in the San Joaquin Valley to 168 m above sea level in the Sierra Nevada foothills. Elevation gradients average about 2.5 m/km on the valley floor and 26.7 m/km in the foothills (Gronberg and Kratzer, 2006). Approximately 55 percent of the lower Merced River Basin is covered by agricultural land; 39 percent is forest, shrub land, and grassland; over 4 percent is urban and transitional land; and less than 2 percent is water and wetland (Vogelmann and others, 2001). The forest, shrub land, and grassland are predominantly on the valley floor.


The San Joaquin Valley is part of the Central Valley, which is a large, northwest-trending, asymmetric structural trough, filled with marine and continental sediments (Bartow, 1991). To the east of the valley, the Sierra Nevada is composed primarily of pre-Tertiary granitic rocks and is separated from the valley by a foothill belt of marine and metavolcanic rocks. The Coast Ranges west of the valley are a complex assemblage of rocks, including marine and continental sediments of the Cretaceous to Quaternary Periods (Page, 1977; Page 1986). Alluvial deposits of the eastern part of the valley were derived primarily from the weathering of granitic instrusive rocks of the Sierra Nevada, and are highly permeable, medium- to coarse-grained sands with low total organic carbon, forming broad alluvial fans where the streams enter the valley. These deposits generally are coarsest near the upper parts of the alluvial fans and finest near the valley trough. Dune sand, derived from the alluvial deposits, consists of well-sorted medium-to-fine sand, as much as 43-m thick (Page, 1986). Stream-channel deposits along the Merced River consist of medium-to-coarse sand with silty-clay layers (~2 cm–60 cm) in the shallow subsurface.

Consolidated rocks and deposits exposed along the margin of the valley floor include Tertiary and Quaternary continental deposits, Cretaceous and Tertiary marine sedimentary rocks, and the pre-Tertiary Sierra Nevada basement complex (Davis and Hall, 1959; Croft, 1972; Page and Balding, 1973). Most of the unconsolidated deposits in the study area are contained within the Pliocene–Pleistocene Laguna, Turlock Lake, Riverbank, and Modesto Formations, with minor amounts of Holocene stream-channel and flood-basin deposits. The Turlock Lake, Riverbank, and Modesto Formations form a sequence of overlapping channel incisions that were influenced by climatic fluctuations, and resultant glacial stages in the Sierra Nevada (Bartow, 1991).

The Corcoran Clay, at the base of the upper Turlock Lake Formation, is a lacustrine deposit that is a key subsurface feature in the San Joaquin Valley. Page (1986) mapped the areal extent of this regional aquitard on the basis of a limited number of well logs and geophysical logs. Additional lithologic data recently were used to modify the mapped extent of this important unit (Burow and others, 2004). The eastern extent of the Corcoran Clay roughly parallels the San Joaquin River valley axis. The Corcoran Clay ranges in depth from 28 to 85 m below land surface and a thickness from 0 to 57 m in the study area.


The San Joaquin Valley has an arid-to-semiarid climate that is characterized by hot summers and mild winters. Average temperatures are fairly uniform over the valley floor. Temperature decreases with increasing elevation in the foothills and mountains of the Sierra Nevada. Long-term records for temperature do not exist for sites within the lower Merced River Basin. However, the Modesto Irrigation District (MID) has temperature data for downtown Modesto from 1939 to 2005 (Modesto Irrigation District, 2005). Mean low temperatures in degrees Fahrenheit range from mid-30s in the winter months to upper 50s in the summer. Mean high temperatures in degrees Fahrenheit range from mid-50s in the winter months to mid-90s in the summer (Gronberg and Kratzer, 2006). As with temperature, long-term precipitation records do not exist within the lower Merced River Basin. However, MID does have long-term precipitation record for Modesto from 1889 to 2005. Mean annual precipitation (1889–2005) in Modesto is 31 cm, but annual precipitation is highly variable. Eighty percent of the precipitation falls during November through March, with the maximum precipitation in December through February.

Surface-Water Hydrology

The surface-water hydrology of the Merced River Basin has been significantly modified by the development of water resources. Between the 1870s and early 1900s, many canals were constructed to transport water to the land. Exchequer Dam was completed in 1926 to provide flood control and water for irrigation and power generation. In 1967, New Exchequer Dam was completed to expand Lake McClure Reservoir’s capacity to 1.26 km3. In the same year, McSwain Dam was completed downstream as a regulating reservoir. Downstream of McSwain Dam, the Merced Falls Dam diverts flow into the MID’s Northside Canal to provide irrigation water to areas north of the Merced River. Farther downstream, Crocker-Huffman Dam diverts flow into the MID’s Main Canal (Stillwater Sciences and EDAW, 2001). The area of focus for this study, the lower Merced River Basin, starts at New Exchequer Dam. Water quality above this point generally is unaffected by agricultural activities. The lower Merced River receives water from Dry Creek and from Mustang Creek by way of the Highline Canal.

Mean annual streamflow measured at the California Department of Water Resources (CDWR) Merced River near Stevinson gaging station (24 km downstream of the study site) is approximately 19.6 m3/s for water years 1941–2005. Mean annual streamflow for this period varies greatly from year to year. The recent water years 2003–2004 had below-normal streamflow, whereas 2005 had above-average streamflow attributed to above-average snow pack in the Sierra Nevada above New Exchequer Dam (fig. 3). In a natural basin, the usual trend is to see a higher streamflow downstream as the area of contribution increases. However, because the Merced River is highly engineered and utilized for agricultural irrigation, it has an overall decrease in streamflow from the upper basin to the mouth.

Ground-Water Hydrology

Ground water in the lower Merced Basin occurs primarily in the unconfined aquifer above and east of the Corcoran Clay and in the confined aquifer beneath the Corcoran Clay. The unconfined aquifer above the clay ranges in thickness from about 40 to 70 m. The unconfined aquifers east of the clay are composed primarily of alluvial sediment, but include the upper part of the Mehrten Formation, which is more consolidated than the overlying formations. The confined aquifer is composed of alluvial sediments and upper Mehrten Formation sediments from beneath the clay to the base of fresh water (Steven Phillips, USGS, written commun., 2006).

Under natural conditions, ground-water recharge occurs primarily at the upper parts of the alluvial fans from streams entering the valley. Prior to ground-water resource development, most ground water had been discharged as evapotranspiration in the central trough of the valley, and to a lesser extent, to streams. Water-resource development in the basin has changed the ground-water flow regime. Pumping for agricultural irrigation and irrigation return flows are much greater than natural recharge and discharge and cause an increase in vertical flow in the system. Ground-water flow is generally toward the southwest and is somewhat similar to the predevelopment flow regime (Gronberg and Kratzer, 2006). However, ground water moving along a horizontal flowpath commonly is extracted by wells and reapplied at the surface several times before reaching the valley trough (Steven Phillips, USGS, written commun., 2006).

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