The dynamics of zooplankton and phytoplankton growth and interactions play a significant role in water quality (e.g., pH and dissolved oxygen [DO]) and the available food supply for higher order organisms in the San Joaquin River Delta. Algae have been shown to significantly impact DO concentrations in the Deep Water Ship Channel (DWSC) of the San Joaquin River (SJR) estuary. Zooplankton grazing is one of the important mechanisms that influence the fate and spatial distribution of algae, and therefore, may contribute to DO deficits that adversely impact aquatic habitat and salmonid migration in the SJR estuary. Numerical water quality models developed to simulate and predict dissolved oxygen in the SJR rely on mathematical algorithms that link chemical and biological mechanisms. Due to the complexity of natural systems, calibrating these models is challenging and often requires independent investigations to estimate input parameters, such as zooplankton grazing and algal growth rates. This investigation explored the applicability of three methods to quantify the rates that zooplankton graze on algae populations in the SJR. Zooplankton grazing studies were performed in the DWSC of the SJR from June 2012 through July 2013. Light and dark bottle microcosm studies using the dilution method, the food-removal method, and the grazer concentration method were tested. A modified microcosm approach similar to the grazer concentration method was developed that yielded changes in chlorophyll a concentrations that were sufficient to separate zooplankton grazing from algal growth and respiration. Microcosms contained zooplankton concentrations that were up to 30 times higher than natural, background levels. Zooplankton grazing rates were consistent in both magnitude and variability with literature values reported for other waters, ranging from 0.295-3.404-m 3 gC -1 d -1 and 0.006-1.413-m 3 gC -1 d -1 for light and dark bottle microcosms, respectively.