Abstract-Agricultural pesticide runoff is a critical issue for many southeastern estuaries. The estuarine microbial food web plays an important role in nutrient cycling and transfer of nutrients to higher trophic levels. The present study examined the effects of agricultural pesticides on the estuarine microbial food web. Polyurethane foam substrates were used to collect microbial communities from a reference tidal creek in the North Inlet National Estuarine Research Reserve (Georgetown, SC, USA). Colonized substrates were brought into the laboratory and exposed to the following commonly used agricultural pesticides: atrazine (and a metabolite, deethylatrazine), endosulfan, and chlorpyrifos. Chlorophyll a, phototrophic carbon assimilation, dissolved oxygen, and phototrophic biovolume were significantly reduced at concentrations of 50 and 250 g/L atrazine and deethylatrazine. Generally, inhibition of the phytoplankton resulted in increased bacterial abundance and productivity, whereas heterotrophic ciliate and flagellate abundances were not affected. Total bacterial abundance, but not heterotrophic bacterial productivity, was significantly reduced with endosulfan treatments of 1 and 10 g/L. Endosulfan was primarily found to target the cyanobacteria. Changes in biomass reflected compositional shifts in the phototrophs. The abundance of heterotrophic ciliates and flagellates was significantly reduced at 10 g/L chlorpyrifos. Bacterial abundance and productivity increased, whereas phototrophic variables decreased. Agricultural pesticides were found to alter both functional and structural aspects of the estuarine microbial food web.