Dissolved oxygen less than 5 mg L(-1) (U. S. EPA advisory level) commonly occurs in the lower San Joaquin River (SJR), California. Most acute episodes typically occur in late summer and fall. The oxygen deficit can stress and kill aquatic organisms, often inhibiting the upstream migration of Chinook salmon (Oncorhynchus tshawytscha). This 5 year study examined watershed-scale spatial and temporal biological oxygen demand (BOD) loads and the primary components believed to contribute to BOD: ammonium, algal biomass, nonalgal particulate organic carbon, dissolved organic carbon, and dissolved organic nitrogen. Samples were collected bimonthly at 15 sites during the summers of 2000 and 2001 and from three lower mainstem sites from May 2002 to March 2005. BOD loads showed a downstream increase in parallel with increasing algal biomass loads resulting primarily from in-stream growth. BOD loads from measured tributaries and drains accounted for 28% and 39% of the BOD load at the downstream Vernalis site in 2000 and 2001, respectively. Algal C was positively correlated (r=0.80) with BOD, explaining 64% of BOD variance for data collected from 2001 to 2005. Less than 20% of BOD was found in the dissolved fraction (<0.45 microm). We conclude that algal biomass is the primary contributor to BOD loads in the lower SJR, upstream of Mossdale.