Following an abnormal flood in 2010 at China’s Poyang Lake, we observed wintering Siberian Cranes Leucogeranus leucogeranus switch from foraging in the shallow-water wetlands they typically use to grassland habitats. These previously undocumented habitat selection patterns raised questions whether differences in crane behaviour such as foraging success existed between the two habitats and how those differences might affect this critically endangered species. Over two winters, we used the density of customary food items (tubers of Vallisneria spp.) obtained from long-term monitoring efforts, Siberian Cranes flock behaviours, individual foraging success and estimated total flock foraging effort across both habitats. Novel foraging patterns by Siberian Cranes were associated with low densities of Vallisneria tubers across multiple sub-lakes within Poyang Lake National Nature Reserve (PLNR). Foraging success was higher in grasslands than in wetlands in winter 2010–2011, but higher in wetlands following a recovery of Vallisneria in 2011–2012. Subsequent to upland foraging during the winter of 2010–2011, we observed lower juvenile to adult ratio of Siberian Cranes at a fall migratory stopover location in north-eastern China despite indications of average environmental conditions in the nesting areas from 2010 to 2012. While grasslands adjacent to shallow-water habitats may be important refugia for wintering Siberian Cranes when Vallisneria is absent or inaccessible, and should be included in protected areas, multi-year dependence on grasslands for foraging could negatively impact population levels. Eliminating crab farming in protected areas and extending protection to shallow water areas sheltered from flooding by dykes could also help secure high quality foraging habitat under a variety of hydrological regimes. Novel foraging patterns by wintering Siberian Cranes represent a new challenge to the conservation efforts for this species that focus on shallow-water wetlands, and may be indicative of broader changes within Poyang’s ecosystem.