Disposal of agricultural drainage has been presenting many challenges in maintaining high agricultural production and environmental health in the hydrologically closed Tulare Basin of San Joaquin Valley, California, because drainage water contains elevated salinity and toxic trace elements including selenium (Se) and arsenic (As). In the evaporation basins under this semi-arid climate, Se was found to be removed from pond waters through several sink mechanisms and mostly accumulated in surface sediments. In contrast, our preliminary investigation indicates that As tends to accumulate in impounded water columns and may become a future possible environmental concern. The objective of this study was to acquire essential data to more fully understand the biogeochemical processes and conditions affecting arsenic accumulation in drainage disposal basins by determining As concentration and speciation in both water columns and sediments. The study site is a 726 ha evaporation basin facility consisting of 10 cells that are operated in series. Pond water chemistry was characterized. Dissolved total As concentration in pond waters increased linearly with increases in salinity and almost linearly with increases in concentrations of Cl. Agricultural drainage water was dominated by arsenate (As, V). Reduced arsenic species, such as arsenite (As, III) and organic arsenic (As, -III), increased following water flow and with salinity. Towards the end of flow path in the terminal cells, water had high dissolved organic carbon and low dissolved oxygen indicating development of a reducing environment. The reducing conditions may have led to reduction of arsenate as a major mechanism affecting the fate of drainage water arsenic disposed into the evaporation basins.