Recent studies showed that climate changes shape species distribution and could cause range shifts in the flyway level of the species. Here, we demonstrated changes in species habitat selection as a response to weather severity in twelve most abundant wintering waterbird species with prevailing increase in numbers during three investigated periods (1972–1978, 1987–1993 and 2003–2009). We used wintering waterbird counts from 93 sites throughout the Czech Republic from mid-January term as the coldest period of winter when the effect of thermoregulation on wintering waterbirds distribution is most apparent. We recorded no significant changes in weather severity in three investigated periods in our study area, and hence we considered the effect of preference of cold weather refuge sites, i.e. habitats which can reduce negative effect of cold weather (running waters, urban area and extensive water surface area). We found prevailing effect of weather severity in the first period what may show thermoregulatory effects being expressed by weather severity on species habitat selection in the next period in six of the twelve investigated species (Mute Swan Cygnus olor, Common Pochard Aythya ferina, Tufted Duck Aythya fuligula, Little Grebe Tachybaptus ruficollis, Common Moorhen Gallinula chloropus and Common Coot Fulica atra). In the face of recent climate change and in spite of the increasing importance of wetlands in the Czech Republic for wintering waterbirds, the suitability of these sites for wintering is likely temperature-dependent. Thus, the preference of cold weather refuges reducing the effect of winter harshness becomes important in individual species.