Pesticides may enter water bodies in areas with a high proportion of agricultural land use through surface runoff, groundwater discharge, and erosion and thus negatively impact nontarget aquatic organisms. The herbicide atrazine is used extensively throughout the Midwest and enters the Mississippi River through surface runoff and groundwater discharge. The purpose of this study was to determine the extent of atrazine contamination in Louisiana's estuaries from Mississippi River water under different flow and nutrient regimes (spring and summer) and its effect on the biomass and oxygen production of the local phytoplankton community. The results showed that atrazine was consistently present in these systems at low levels. Microcosm experiments exposed to an atrazine-dilution series under low and high nutrient conditions to determine the phytoplankton stress response showed that high atrazine levels greatly decreased phytoplankton biomass and oxygen production. Phytoplankton exposed to low and moderate atrazine levels under high nutrient conditions were able to recover after an extended acclimation period. Communities grown under high nutrient conditions grew more rapidly and produced greater levels of oxygen than the low nutrient treatment groups, thus indicating that atrazine exposure may induce a greater stress response in phytoplankton communities under low-nutrient conditions. The native community also experienced a shift from more sensitive species, such as chlorophytes, to potentially more resilient species such as diatoms. The phytoplankton response to atrazine exposure at various concentrations can be especially important to greater trophic levels because their growth and abundance can determine the potential productivity of the entire ecosystem.