In this study we have used stable isotope analysis to identify major food resources driving food webs in commercial rice agroecosystems and to examine the effects of agricultural management practices on the trophic structure of these food webs. Potential carbon sources and aquatic macroinvertebrate consumers were collected from large-scale rice farms in south-eastern Australia cultivated under three different crop management regimes conventional-aerial (agrochemicals applied, aerially sown), conventional-sod (agrochemicals applied, directly sown) and organic-sod (agrochemical-free, directly sown). Evidence from stable isotope analysis demonstrated the importance of food sources, such as biofilm and detritus, as the principal energy sources driving aquatic food webs in rice agroecosystems. Despite the greater diversity of potential food sources collected from the organic-sod regime across all sampling occasions, the range of food resources directly assimilated by macroinvertebrate consumers did not differ substantially across management regimes. Trophic complexity of aquatic food webs, as evidenced by the number of trophic levels identified using '15N data, differed across management regimes at the early season sampling. Sites with low or no agrochemical applications contained more than two trophic levels, but at the site with the highest pesticide application no primary or secondary consumers were found. Our data demonstrates that the choice of agricultural management regime has a season-long influence on aquatic food webs in rice crops, and highlights the importance of conserving non-rice food resources that drive these trophic networks.