We analyzed population trends of 13 waterfowl (Anseriformes) species wintering in Japan during a 14-year period (1996–2009). We used data from annual volunteer-participatory waterfowl count surveys which were conducted in Japan by the Ministry of the Environment and local prefectural governments. Population indices and long-term trends of each species were calculated using TRIM (TRends and Indices for Monitoring data). TRIM is a freeware program developed for analysis of time series count data with missing observations. During the 14 years, seven species exhibited significant long-term declines, while four species showed long-term increases. Most of the species that showed long term declines were characterized as being water-surface foraging species, species breeding in both middle and high latitude regions, or species using rice fields. Most species that showed long-term increases were characterized as diving species, species breeding at high latitude or species rarely using rice fields. We calculated composite indices for these groups. The group of water-surface foraging species showed declines in river, natural lakes and artificial lakes, except reservoirs, when each habitat was analyzed separately. In contrast, the group of diving foraging species showed an increase in estuarine habitat. We suggest that changes in: water quality, breeding habitat in the middle latitude region, and in cultivation methods in rice fields, have affected population changes of some species and groups.