This study investigates the toxicity and post-exposure effects of dissolved microcystin (MC-LR) on the dominant copepods of the upper San Francisco Estuary (SFE), where blooms of the toxic cyanobacteria Microcystis aeruginosa coincide with record low levels in the abundance of pelagic organisms including phytoplankton, zooplankton, and fish. The potential negative impact of Microcystis on the copepods Eurytemora affinis and Pseudodiaptomus forbesi has raised concern for further depletion of high quality fish food. Response of copepods to MC-LR (MC) was determined using a 48-h standard static renewal method for acute toxicity testing. Following exposure, a life table test was performed to quantify any post-exposure impacts on survival and reproduction. The 48-h LC-50 and LC-10 values for MC were 1.55 and 0.14 mg/L for E. affinis; and 0.52 and 0.21 mg/L for P. forbesi. Copepod populations recovered once dissolved MC was removed and cultures returned to optimal conditions, suggesting no post-exposure effects of MC on copepod populations. Dissolved microcystin above 0.14 mg/L proved likely to have chronic effects on the survival of copepods in the SFE. Since such high concentrations are unlikely, toxicity from dissolved microcystin is not a direct threat to zooplankton of the SFE, and other mechanisms such as dietary exposure to Microcystis constitute a more severe risk.