Pesticide use affects aquatic communities directly and indirectly. Previous work showed morphological and neurodevelopmental changes in tadpoles exposed to the pesticide chlorpyrifos (CPF; 5 and 20ppb) in mesocosms. It is unclear if effects resulted from direct CPF exposure or from trophic interactions due to a decline in zooplankton. This study aimed to determine if CPF affects brain anatomy when the trophic environment is not altered and to determine the extent of protection that pesticide-resistant zooplankton have on an aquatic community. Lithobates pipiens tadpoles were exposed to 0ppb or 1ppb CPF and then reared to metamorphs in mesocosms containing either CPF-resistant or CPF-sensitive Daphnia pulex zooplankton. In mesocosms with CPF-sensitive zooplankton, relative body length and head width of metamorphs was reduced; the reverse was found in metamorphs from mesocosms with CPF-resistant zooplankton. Exposure to CPF resulted in metamorphs with relatively wider optic tectum, medulla, and diencephalon compared to controls, regardless of whether zooplankton was CPF-resistant. Hence, survival of zooplankton in the presence of CPF stabilizes the food web and can have buffering effects on metamorph body shape, but protecting the food web did not mitigate the effects of CPF on metamorph brain morphology. This study provides evidence of the dangers of exposure to low, ecologically relevant doses of organophosphorous pesticides on neurodevelopment in vertebrates.