Analyses were made for dissolved constituents including selenium (Se) in waters associated with subsurface agricultural drainage from the western San Joaquin Valley of California. In the vicinity of Kesterson National Wildlife Refuge and the Grassland wetlands area Se was found to be mobilized in water. As a consequence of this mobility and bioaccumulation in the aquatic food chain, Se occurred in waterfowl at levels toxic enough to cause deformities and deaths. Se concentrations in sumps that collect subsurface agricultural drainage water and inflows to drains sampled, ultimately leading into Kesterson National Wildlife Refuge and the Grassland, ranged from 84 to 4200 microgram/L (ug/L) Se. Levels of Se were reduced in the San Luis Drain flowing into Kesterson National Wildlife Refute to approximately 300 ug/L Se and in three of the drains sampled flowing into the Grassland to approximately 50 ug/L Se. Serious effects on water fowl habitat were caused by both these levels. Se contents of algal mats and salt crusts from evaporation ponds of the San Luis Drain contained up to parts per million Se. Total ecosystem assessment of Se may be necessary for the evaluation of the toxicity of Se to the environment. No other trace element reported exceeded the various criteria for water at the level of magnitude of Se. Other dissolved constituents and the isotopic ratios of oxygen and hydrogen were analyzed to elucidate water types, reaction states of the aqueous solution with respect to minerals, and the origin of mixed waters. These data will be used later to evaluate the geologic source of Se. Methods used for collection and analysis are described and documented. Hydrologic effects were found to be complex. Preliminary indications from wells are also given. A historical sequence is adhered to and other data from the study area which serve as a guide to the toxicity of Se are included. (Author 's abstract)