To investigate the effect of organic farming on food intake and abundance of three egret and heron species (Great Egret Ardea alba, Intermediate Egret Egretta intermedia, Grey Heron A. cinerea), field surveys were conducted in conventional and organic rice fields in five cities in Ibaraki and Tochigi prefectures, Japan, from May to July 2013 and 2014. Direct observation of prey captures revealed that fish (mainly Oriental Weather Loach Misgurnus anguillicaudatus) and frogs Rana spp. are the primary food sources, although their compositions differed among bird species; proportion of fish biomass was higher in the order of Great Egret, Intermediate Egret and Grey Heron. In addition, for all three species, composition of fish mass in organic fields was higher than that in conventional ones. Generalized linear models showed that organic farming had a positive effect on food intake rates (g/min) although the effect seemed to be clear only for Great Egret. Organic farming also had a positive effect on the abundance of foraging Great Egrets and Grey Herons. Therefore, we concluded that the benefit of organic farming was consistently shown for Great Egret, but not for Intermediate Egret and Grey Heron, possibly due to differential effects of rice pesticides on prey species (e.g., fish and frogs) and the small area of organic rice fields in Japan (only 0.28% of rice fields are managed for organic farming in Japan amounting to 18-68% of census plots in this study).