Since the discovery of selenium toxicosis in the Kesterson Reservoir in the San Joaquin Valley, California, public perception of irrigated agriculture as a benign competitor for California's developed water supply has been changed irrevocably. Subsurface return flows from irrigated agriculture were implicated as the source of selenium which led to incidents of reproductive failure in waterfowl and threatened survival of other fish and wildlife species. Stringent water quality objectives were promulgated to protect rivers, tributaries, sloughs and other water bodies receiving agricultural discharges from selenium contamination. Achieving these objectives was left to the agricultural water districts, federal and state agencies responsible for drainage and water quality enforcement in the San Joaquin Basin. This paper describes some of the strategies to improve management of water resources and water quality in response to these new environmental objectives. Similar environmental objectives will likely be adopted by other developed and developing countries with large regions of arid zone agriculture and susceptible wildlife resources. A series of simulation models have been developed over the past four years to evaluate regional drainage management strategies such as: irrigation source control; drainage recycling; selective retirement of agricultural land; regional shallow ground water pumping; coordination of agricultural drainage, wetland and reservoir releases; and short-term ponding of drainage water. A new generation of Geographic Information Service-based software is under development to bridge the gap between planning and program implementation. Use of the decision support system will allow water districts and regulators to continuously monitor drainage discharges to the San Joaquin River in real-time and to assess impacts of management strategies that have been implemented to take advantage of the River's assimilative capacity for trace elements and salts.