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• What is the woooeility that normal reservoir operations will lead to a shortfall from contractual water deliveries or reservoir pool elevations falling below some critical level in the current water year? How would a modified operation over the next week change this probability? • How would a new reservoir release schedule (focused on diurnal and weekly fluctuations) affect hydropower peaking revenue, channel geometry, beaches, recreational opportunities, and habitat for sport fish or an endangered species? • How would a major land-use change in the basin (related to logging, urbanization, or agriculture) affect water availability? How would changes in climate (storm tracks, temperature) affect water availability? • How could ground-water pumpage, reservoir releases, and artificial ground-water recharge operations be optimized to maintain ground-water quality and desired water levels? USGS efforts in this joint program include (1) further research, development, and refinement of hydrologic modeling tools, including writing new computer programs, supporting and documenting existing programs, and providing training in the use of the models; (2) research on hydrologic processes, the results of which would be incorporated into the models to improve the reliability and scope of the predictions; and (3) basin-specific development and calibration of hydrologic models to the selected river basins for case studies. Research topics include aspects of snow accumulation and melt in mountainous areas, changes in channel morphology that result from changes in sediment supply and flow regime, long-term changes in reservoir water quality (salinity and eutrophication), and consequences of soil drainage and ground-water development on salinity and trace-element contamination. The Bureau of Reclamation’s efforts focus on development and improvement of data-management and modeling tools, which include modeling of system operations, water management and deliveries, and the hydraulics of water delivery to agricultural fields and the subsequent drainage and evaporation from those fields. Specific topics include water use, land use, simulation of the water rights system, balancing project benefits, optimization of system operations, stochastic hydrologic modeling, runoff forecasting, realtime operational modeling, and expert system techniques. As the models become operational, the Bureau of Reclamation plans to

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integrate them into current basin-management systems.

Both bureaus are working together to ensure that the data and models from one bureau interact efficiently with those from the other and on basin-specific model calibration and implementation. They also are developing integrated training activities in support of the program.

A pilot study is currently underway in the San Juan River Basin, which is centered in the Four Corners area of Utah, Colorado, Arizona, and New Mexico. The major management issues relate to streamflow regulation and endangered fish, competition for water, and Native American water rights. The final product of this pilot study will be an integrated system of models, databases, and decision-support tools implemented within the operating systems of the Bureau of Reclamation and other agencies responsible for aspects of river-basin management. The models, databases, and decision-support tools will be thoroughly documented by user manuals and technical reports in the scientific and engineering literature. The central focus of the integrated systems will be a river-basin model capable of predicting the timing and amount of runoff and simulating the operations of reservoirs and diversions according to specified operating rules. The models will be used to assess the risk of water shortage or flooding over a period of months to years. They also will be used to assess the changes in these risks associated with changes in the operating policies or in the physical infrastructure.

Harry F Lins administers the USGS Watershed Modeling Program and the Global Change Hydrology Program.

The San Juan River Basin of Utah, Colorado, Arizona, and New Mexico and associated water-management issues. Improved watershed modeling systems are being applied directly to these issues and others being faced by watermanagement organizations in the Western United States.

For more information on watershed modeling, contact Harry Lins at:

Telephone: (703) 648-5712

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feet apart have developed at land surface
above the two collapsed mine rooms. The
northernmost feature, which is about 700 feet
in diameter, includes a central area that is
about 200 feet wide and has subsided about
20 to 30 feet. The southernmost feature,
which is about 900 feet in diameter, includes
a central area that is about 700 feet wide and
has subsided about 70 feet. The subsidence in
the collapse area has forced the closure of a
section of State Route 20A as a result of the
partial collapse of a State Department of
Transportation bridge.
During the formation of these collapse
features, hydraulic connections formed
between aquifers that previously had been
isolated from each other by confining units.
These new connections have provided routes
for rapid migration of ground water down-
ward to the mine level. Since March 12,
ground water draining from overlying aquifer
systems has been progressively flooding the

tudy area
study are A Well that had
rapid dewatering
or had gone dry
as of August 1994
|Genesee River Valley
|Genesee Uplands
Well in basal gravel | Route 63


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Collapse area


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mine at inslow taxes overaging about 18,000 gallons per minute.") his aquifer drainage has caused inadequate water supplies in a number of local wells, some of which have actually gone dry. Land subsidence that might be related to compaction due to aquifer drainage has occurred near Mt. Morris, about 3 miles southwest of the collapse area.

The U.S. Geological Survey (USGS) has been working with the Livingston County Department of Health since March 1994 to provide technical expertise in dealing with this situation. A regional ground-water-levelmonitoring network has been established to observe the rate, magnitude, and extent of aquifer drainage related to the mine collapse. Water levels in some wells drilled in the floodplain sediments and upland bedrock units are showing only expected seasonal changes since the collapse. Water levels in some wells drilled in glacial deltaic deposits and a basal gravel on top of the bedrock surface, however, show significant declines that are a result of the aquifer drainage.

A conceptual model of the groundwater-flow system has been developed on the basis of knowledge of the hydrogeology of similar valleys in central and western New York, borehole geophysical surveys of 18 wells drilled in and adjacent to the collapse features, and marine seismic-reflection profiling on the Genesee River. The complex ground-water-flow system involves multiple aquifers in the glacial sediments and the bedrock.

In June 1994, a team of specialists from the USGS examined the environmental effects of the partial collapse of the mine. They compiled a list of recommendations for further short- and long-term studies to address the major issues of public safety, aquifer drainage, and subsidence.

The USGS continues to monitor ground-water levels in the area and is constructing a preliminary numerical model to assess the long-term impacts of the partial mine collapse on the regional ground-waterflow system.

Dorothy Tepper

is Project Chief of the Retsof Salt Mine study and has studied ground-water flow in glacial sediments and bedrock for the past 15 years.

Todd Miller

has studied glacial geology and ground-water flow in glacial sediments for the past 16 years.

Bill Kappel has studied the interactions of surface water and ground water for the past 21 years.

John Williams is the ground-water specialist for the New York District and a borehole geophysics advisor.

The San Francisco Bay and Delta: An Estuary Undergoing Change

he San Francisco Bay Estuary, which is at

the confluence of the Sacramento and San Joaquin Rivers in central California, is renowned for its natural beauty, international commerce, recreation, and sport fishing. However, the estuary has been greatly modified by 150 years of intensifying human activity.

The U.S. Geological Survey (USGS), recognized internationally for its interdisciplinary expertise and experience in the study of estuarine processes and as a long-time leader in studies of the San Francisco Bay Estuary, has provided much of the fundamental knowledge about interrelations among the hydrology, geology, chemistry, and ecology of this complex estuarine system. For example, USGS studies have documented changes in the estuary's shoreline; changes in patterns of water and sediment movement; contamination of its water, sediments, and organisms; and alterations of biological communities. The USGS is now focusing field, laboratory, and modeling studies on the effects of freshwater flow on the estuary's chemistry and biology, the distribution and influence of contaminants on estuarine invertebrates, and the processes that influence the character and stability of the remaining wetlands.

More than 95 percent of the historical tidal marshes have been leveed and filled, the result being losses in fish and wildlife habitat. The flow of freshwater into the estuary has been greatly reduced by water diversions to support, for the most part, irrigated agriculture. Harbor and channel dredging has changed the dredged areas and disposal sites and altered water-flow patterns and salinity. Contaminants enter the estuary in municipal and industrial sewage and urban and agricultural runoff. Introduced exotic species continue to change the bay's biota by altering its

For more information on the Retsof Salt Mine project, contact Dorothy Tepper at:

Telephone: (607) 266–0217

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It is not clear which and to what extent particular human activities are responsible for specific unwanted ecosystem changes. Thus, determining which courses of action would be most effective in bringing about improvements in the estuary's water quality and restoration of its fish populations has been difficult. Potential limitations to additional economic development include demands on land and water supplies, increasing constraints on diverting water away from the delta because of concerns for endangered species, pressures to shift consumption of managed water from agricultural use to urban use, future land subsidence as a result of

increasing dependence on ground-water supplies in dry years, further loss of tidal wetlands to urban encroachment, and constraints on harbor improvements because of potential changes in salinity and contaminant levels as a result of dredging and spoils disposal.

Conflicts among the many uses of the bay/delta system have led resource managers and regulators, elected officials, and the public to recognize the need for credible, unbiased scientific information on the significance of river-flow diversion, contaminant inputs, dredging, and habitat alteration.

Effects of Freshwater Flow

hanges in the quantity, timing, and

quality of freshwater that flows into the delta and the bay as a result of diversion by means of pumps within the delta are implicated in declines of fish species. Young fish are physically removed by the pumps, and changing flow patterns and salinity distributions create habitat changes. The U.S. Environmental Protection Agency has proposed a salinity standard that would require the salt content of the water in ecologically sensitive regions of the estuary to be maintained at specified levels. There is need for a better quantitative understanding of flow patterns and salinity distributions within the delta and Suisun Bay and the relations between the two.


The USGS has conducted broad-scale field and modeling studies of water movement and salinity distributions within the estuary. In cooperation with other agencies in the Interagency Ecological Program (IEP), the USGS is applying new technologies to measure within-delta water transfers and delta outflow into the bay, providing information needed for documenting salt-transport mechanisms, and managing freshwater flow to meet salinity standards. The USGS also is developing statistical models to relate anomalous precipitation, snowpack, temperature, and atmospheric circulation to combined monthly flows in the Sacramento and San Joaquin Rivers.

The relation between freshwater flow and contaminant transport to and through the estuary is important. For example, USGS studies have detected pulses of pesticides (applied during winter in the Sacramento and San Joaquin Valleys) that flow through the delta and upper estuary during winter runoff. These pesticide pulses reach concentrations that have been shown to be toxic to aquatic life in the delta and Suisun Bay. At the same time, sediments and sediment-bound contaminants are being transported through the delta into the bay. The mechanisms of dissolved contaminant and sediment transport in the bay must be understood in order to estimate organism exposure and evaluate mitigation alternatives.

Correlations between flows and most biological populations in the bay and the delta are well documented. For example, scientists know that river flow is a source of organic matter supporting biological productivity within the estuary and that transfers of organic matter among different levels of the food web are influenced by fluctuations in freshwater inflow. They also know that flow conditions are implicated in ecological disruptions (major changes in the estuary's food web) that follow invasions by exotic species. Unfortunately, many of the underlying causes of these changes have not been identified. In particular, establishing the connections between flow-related habitat features and the sustainability of individual fish populations is a high priority. The USGS maintains a baseline measurement program (mapping temperature, salinity, turbidity, and chlorophyll in the channel and emphasizing sampling of benthic invertebrate species abundances and phytoplankton blooms) in San Pablo Bay, Central Bay, and South Bay that

complements the IEP program in the upper estuary and delta. Additionally, USGS laboratory experimentation and modeling efforts are providing an understanding of the couplings between water and sediment movement, the biogeochemical cycling of nutrients, the population dynamics and primary production of phytoplankton, and the establishment of introduced species.

Distribution and Effects of Contaminants

Co. from numerous sources are pervasive throughout the estuary and its watershed. Agencies charged with protecting and enhancing the estuary's biological resources recognize the need for a much better understanding of contaminant distribution and ecological effects. The USGS is examining trace-metal and pesticide concentrations in sediments and benthic invertebrates to provide this understanding. For example, the biological effects of pesticides entering the bay during high river flows are being examined by conducting laboratory toxicity tests on local invertebrate species. The USGS also is using models and field studies to investigate recycling of metals and nutrients from internal sedimentary sources in the estuary. In cooperation with the San Francisco Regional Water Quality Control Board and the U.S. Army Corps of Engineers (COE),

the USGS also is quantifying the physical fac

tors (for example, tidal currents and wind waves) that control resuspension and transport of fine sediment in the shallows of the bay to assess the importance of resuspension events on metals concentrations in the water.

Wetlands Processes

he loss of 95 percent of the estuary's

wetlands since 1850 has increased the importance of the remaining 125 square kilometers, which continue to be threatened by development, erosion, pollution, and rising sea level. Wetland management agencies (for example, the COE and the San Francisco Bay Conservation and Development Commission) must develop viable strategies for creating new wetlands in leveed areas used as farmland or as salt-evaporation ponds that have subsided since being isolated from bay

Agencies participating in the Interagency Ecological Program include the U.S. Fish and Wildlife Service, the Bureau of Reclamation, and the U.S. Geological Survey (all bureaus in the Department of the Interior), the U.S. Army Corps of Engineers, the U.S. Environmental Protection Agency, the California Water Resources Control Board, the California Department of Water Resources, and the California Department of Fish and Game.

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