In Japan, Rice Oryza sativa fields are regarded as important sites for wintering waterbirds. Rice fields harbor considerable amounts of post-harvest waste rice, which is an important food resource for dabbling ducks in winter. The availability of rice fields as duck foraging sites is affected by agricultural management methods, harvest methods or post-harvest treatment of residues. In the present study, we examined the effects of two agricultural practices after harvesting, flooding with shallow water and plowing the surface of fields, on foraging site selection by ducks in rice fields near Katano-kamoike, Ishikawa Prefecture, Japan. To investigate the distribution of duck flocks in rice fields, night censuses were conducted during winters 2004–2005 to 2006–2007. Field conditions (flooded or plowed) in the census area were also recorded. By GLMM model selection, it was shown that water cover had a positive effect on the number of ducks, but post-harvest plowing had a negative effect. Furthermore, the effect of plowing was tested by a field experiment. The initial grain density on the ground was higher at unplowed plots. Unplowed rice fields are considered to be more suitable for ducks as foraging sites, with plowing reducing the attractiveness of rice fields as foraging sites by burying residual rice grains.