Lake Izunuma-Uchinuma in northern Japan experienced extensive flooding in July 2022, resulting in significant damage to the vegetation of the lotus Nelumbo nucifera. Lake Izunuma which has an area of 357 ha, was 62% covered by lotus vegetation in October 2021, but only 11% in September 2022. Whooper Swans (Cygnus cygnus) that winter in Lake Izunuma-Uchinuma forage mainly on the rhizomes of the lotus. The number of Whooper Swans wintering from November 2022 to January 2023 decreased significantly compared to the preflood season of 2021/2022. The number of swans in Lake Izunuma-Uchinuma decreased significantly compared to the populations of swans at other wintering sites, despite the fact that the daily average temperatures at the three sites on the migration route of the swans did not differ significantly between these seasons. The significant decrease in lotus vegetation caused by flooding in July 2022 is considered the cause of the decrease in the number of Whooper Swans wintering on the lake in the 2022/2023 season.