Pesticide use is known to have a negative impact on the habitat use of birds. The decomposition of residual pesticides causes a drastic decrease in the biomass of wildlife food sources, indirectly affecting the ecosystem. In this study, we investigated the effects of pesticide use on the distributions of grey herons (Ardea cinerea) and great egrets (Ardea alba) in rice fields in the Republic of Korea. From early May to mid-June in 2015 and 2016, we recorded the abundance of these birds and their prey (loaches, other fish, tadpoles, and benthic invertebrates) and investigated their dependence on rice agricultural practices (eco-friendly vs conventional) and field types (harrowed, plowed, or transplanted). We found that both grey herons and great egrets preferentially used transplanted fields. Grey herons were observed more in conventional rice fields, while great egrets were observed more in eco-friendly rice fields. This may be driven by the distribution of their preferred prey types; we observed a higher density of tadpoles (the prey type favored by grey herons) in conventional fields and a higher density of loaches (the preferred prey of great egrets) in eco-friendly fields. Pesticides drive these patterns both directly and indirectly; pesticide use in conventional rice fields directly suppresses the abundance of loaches, which frees the tadpole population from predation pressures and indirectly boosts their abundance in conventional rice fields. Our findings suggest that the distributions of grey herons and great egrets vary depending on food availability and are directly and indirectly influenced by pesticide use.