Despite wetland conversion to intensive rice production Central Thailand remains a center for wetland biodiversity in Southern Asia. Fauna inhabiting rice fields (many species perform important ecosystem services) are, however, increasingly threatened by pesticide uses. In Ayutthaya and Ang Thong Provinces 40 conventionally and 31 organically managed farms were visited to investigate how abundance and diversity of aquatic fauna in rice fields relate to pesticide regimes. In the dry and wet seasons fields were surveyed for plankton, aquatic macro-invertebrates, fishes, and waterfowl. Using multivariate statistics pesticide variables and biophysical field parameters (determined in a previous study) were assessed as potential predictors of abundance/diversity of faunal groups. Effects of pesticide regimes on aquatic fauna were nontrivial. Phytoplankton was lowered under exposures to herbicides and natural insecticides. Zooplankton (except amoeboids) was unaffected or increased on pesticide-exposed fields, probably suffering lower predation. Biophysical aspects partly explained abundance/diversity of aquatic insects, but abundance/diversity was generally higher on fields treated with natural rather than synthetic insecticides. Fishes and waterfowl tended to be less abundant on fields exposed to synthetic insecticides and herbicides. Detailed findings may interest agro-ecologists, medical entomologists, and conservation biologists. Further research incorporating wider landscape aspects and including pesticide-free reference sites is suggested.