The San Joaquin River is a hypereutrophic river, flowing through one of the most productive agricultural regions of California. Spatial and temporal water quality dynamics were investigated using three different sampling strategies (bi-monthly, fixed-point diel, and Lagrangian) in the lower San Joaquin watershed with the goal to understand how the upstream sources that contribute to low dissolved oxygen levels in the Stockton Deep Water Ship Channel (DWSC), and how the variation in key water quality constituent concentrations depends on when and how the water was sampled. Ammonium, algal biomass, non-algal particulate matter, dissolved inorganic carbon, and dissolved inorganic nitrogen were the investigated as the primary contributors to biological oxygen demand (BOD) in the DWSC. Identification of algal biomass as the primary contributor to BOD resulted in the exploration of sampling strategies to best establish Total Maximum Daily Load (TMDL) requirements. Diel (24 h) sampling at two fixed locations on the main-stem of the river revealed sinusoidal diel patterns for algal pigments, fluorescence, temperature, dissolved oxygen, pH, volatile suspended solids, dissolved inorganic nitrogen, and soluble reactive phosphorus. Algal nutrient uptake explained the day-time decreases in nutrients; however, the observed night-time algal decrease could not be explained by herbivory, death, or respiration. In order to explain the night-time algal decrease observed at a fixed location, a parcel of water was sampled as it traveled downstream (Lagrangian) in a concrete-lined agricultural drain which empties into the San Joaquin River. Sinusoidal diel patterns occurred only in dissolved oxygen, pH, and temperature. Algal pigments, nutrients, suspended solids, and turbidity did not show sinusoidal diel patterns, an indication the sinusoidal diel pattern observed at a fixed sampling location was a result of day-time algal growth and transport processes. The results from this study provide information to assist in developing appropriate monitoring protocols to meet TMDL requirements, and to capture the variability which occurs within a parcel of water as it travels downstream.