Low dissolved oxygen occurs seasonally in the lower San Joaquin River of California where it stresses or kills aquatic organisms and often inhibits upstream migration of fall-run Chinook salmon. Algal biomass was shown to be the primary component contributing to biological oxygen demand imports from the agriculturally dominated upstream watershed. The primary objective of this study is to examine spatial and temporal algal dynamics in the lower San Joaquin River. Centric diatoms dominate the total algal biovolume in the mainstem of the San Joaquin River, with Cyclotella meneghiniana being the dominant species. High concentrations of available nutrients result in the algae growth being light limited with a photic zone (~1% light penetration) of about one meter during the summer. The majority of algal biomass results from in-stream growth in the mainstem rather than from inputs from tributaries and agricultural drains. However, inputs from upstream agricultural drains provide a steady inoculum (seed source) to fuel downstream growth. Changes in chlorophyll-a concentrations display strong temporal patterns at the inter-annual, seasonal and diel time scales. Diel variation in chlorophyll-a concentrations (~100 ppb) during the summer was as large as the seasonal variation in the daily mean chlorophyll-a concentrations. Diel chlorophyll-a concentrations display an approximate doubling with a maximum at sunset and a minimum during the mid-morning. The mechanism for the diel pattern is day-time algae growth followed by night-time advection (transport) of algae in the absence of growth. This study suggests that reducing algae seed source from upstream agricultural drains could be an effective mechanism to reduce algal biomass inputs into the lower San Joaquin River where hypoxia occurs. The use of slow-moving, flow-through wetlands with ample vegetation to shade the water column could provide a low-cost management practice to remove algae seed source prior to discharge into the San Joaquin River.