We analyzed existing records of the presence and breeding of three water bird species (Little Grebe Tachybaptus ruficollis; Common Moorhen Gallinula chloropus; and Spot-billed Duck Anas zonorhyncha) at 1,087 ponds in Osaka Prefecture to estimate the effects on them of various environmental, geographical, and social factors. A conditional autoregressive (CAR) model, incorporating spatial structure as a random effect, was applied in the analyses. Results show a significant positive effect of a broad shape of the water surface, which indicates the importance of threats by terrestrial enemies, on the probability of the presence of each species. Two human social factors affected the probability of breeding of two bird species: human population density negatively affected the breeding probability of T. ruficollis and A. zonorhyncha; and the retail store density, an index of development as a commercial area, positively affected the latter species. Spatial random effects reflecting unmeasured factors were large and comparable to other measured factors. Different patterns were exhibited among the three species, demonstrating that other important factors were overlooked and that these effects should be assessed by application of methods such as the CAR model.