Elements of an environmental decision support system for seasonal wetland salt management in a river basin subjected to water quality regulation Page: 2 of 16

                                
teratogenicity in waterfowl embryos. Free of harmful concentrations of selenium, wetland
water supply is now supplied by canal from the Sacramento - San Joaquin River Delta but still
contains inorganic salts which evapoconcentrate in the man-made, seasonally managed ponds,
before being drained (between late March and early May) into channels that flow into the San
Joaquin River. The wetland drainage (drawdown) schedule often coincides with the
germination period of salt sensitive agricultural crops, irrigated with water pumped from the
River more than 100 km downstream in the South Delta. Seasonal wetland drainage produced
within a 50,000 hectare wetland Ecological Complex, known as the Grasslands Ecological
Area (GEA) must be eliminated to preserve salt balance and preserve habitat conditions that
make them the most important migratory bird resource in the western United States. During
dry and critically dry years dilution flows from the Sierran tributaries to the San Joaquin River
(SJR) diminish and can no longer prevent frequent violations of the State water quality
objectives for salinity from occurring. The compliance monitoring station for salinity on the
SJR is located at a site immediately upstream of any tidal influence.
Recent environmental regulation promulgated as Total Maximum Daily Loads (TMDL's) limit
agricultural discharges of salt loads to the SJR - drainage salt loads from seasonally managed
wetlands are subject to the same numerical constraints. During dry and critically dry years the
salt TMDL is especially restrictive allowing no salt load export to the SJR during the summer
months when drainage return flows are typically highest and the impacts due to restricted
drainage most severe. Seasonally managed wetlands, which mostly drain during the months of
March and April each year will also be restricted in their drainage salt load export to the River.
These restrictions could have significant impacts on wetland habitat quality and their long-term
resource potential as overwintering habitat for waterfowl.
Real-time water quality management (RTWQM) has been advocated as a means of improving
SJR water quality by better coordinating the discharge of salt loads from west-side San
Joaquin Basin agricultural, wetland and municipal dischargers with east-side San Joaquin
Basin reservoir releases and irrigation return flows that provide dilution. RTWQM is a concept
that relies upon access to real-time flow and water quality data from networks of flow and
water quality (electrical conductivity and temperature) sensors on the SJR (Quinn and
Karkoski, 1989) and which involves watershed flow and water quality modeling, salt
assimilative capacity forecasting in the SJR and information dissemination as part of an
Environmental Decision Support System (EDSS).
The ultimate goal of projects underway in support of RTWQM is to develop a comprehensive
monitoring and modeling system that provides timely decision support to agricultural water
districts and seasonal wetland managers - allowing them to improve the coordination of salt
load export with the available assimilative capacity of the San Joaquin River (Quinn and
Hanna, 2003). Although salinity management has been practiced within west-side San Joaquin
River Basin agricultural water districts for more than 100 years and salinity management has
only become a concern to seasonally managed wetlands since the announcement of the salt
TMDL - progress towards RTWQM is more advanced in the wetland areas. This is largely

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