The Geum River, Republic of Korea, is an important wintering site for waterbirds that migrate along the East-Asian Australasian Flyway. It has recently experienced two major changes in environmental conditions as a result of increased use of bale silage (wrapping and sealing forage crops with plastic bags during harvest) beginning in 2007, and the Four Major Rivers Restoration Project (FMRRP) in 2011 to deepen and widen the major rivers in Republic of Korea. To examine these effects on wintering waterbirds, we monitored changes in wintering waterbird abundance in the downstream and upstream regions of Geum River. Wintering waterbirds in the downstream region were reduced by 67% after use of bale silage compared to before bale silage. The FMRRP changed the habitat structure, deepening and widening the river, followed by a substantial decline in overall wintering waterbirds in both regions (38% in the downstream and 51% in the upstream). Mallard (Anas platyrhynchos) and Spot-billed Duck (A. poecilorhyncha) populations showed the most decrease in numbers. However, Common Mergansers (Mergus merganser), that fish in deep water, increased over the same time. The effects of such changes in habitat conditions are not temporary, elucidating the need for monitoring and conservation programs for wintering waterbirds.