A total maximum daily load (TMDL) for oxygen demanding substances is being implemented in the San Joaquin River (SJR) in California (USA) due to frequently occurring low dissolved oxygen conditions. The SJR is a eutrophic river, heavily impacted by agriculture. A mass balance was developed to identify the sources of oxygen-demanding substances and nutrients to the river with the objective of providing a scientific basis for management actions needed to meet TMDL requirements. Data were collected for flow and water quality and mass loads calculated for sites within the main stem of the SJR, river inputs (tributaries), and diversions in the study area. Using a quadrant analysis, tributary flows and loads are ranked to identify targets for water quality improvement efforts. Additionally, all mass loads were summed (inputs minus diversions) and compared with observed loads at the downstream limit of the study area. The mass balance analysis identifies major contributors of mass loads and mass balance closure is assessed for each constituent. These analysis methods inform the TMDL process which includes a load allocation, and is useful for determining locations for implementation of improvement projects needed to improve the health of the river.