Over the course of a year, rice fields display spatial and temporal differences according to farming management practices, providing a succession of habitats throughout the crop-growing cycle for various waterbird species. However, few studies have assessed the influence of the spatial and temporal differences produced by rice field farming management practices on waterbird species during a year. The present study investigated spatial and temporal patterns of species distribution and examined the factors that affect waterbird selection of foraging habitats in the rice fields located in the midwestern part of South Korea from April 2009 to March 2010 and from April 2011 to March 2012. Waterbird species represented strong seasonality and selectively used different field types at a fine spatial scale. The selection of field type depended more on field structures that were related to the vulnerability of prey items than on prey abundance in rice fields. Water level was an important factor that affected shorebird selection of foraging habitat, and they chose habitats with different water levels according to their body size. The density of rice plants was a critical factor affecting the selection of habitats by herons, because densely planted fields inhibited their access to food. The presence of rolled straw in rice fields affected the distribution of waterfowl. These results demonstrate that farming management practices, which determine prey accessibility, strongly affect the use of rice field habitats by waterbirds. Our knowledge of these relationships should be incorporated into conservation practices protecting the various waterbird species that use rice fields.