Studying the changes in extreme river runoff induced by climate change is of utmost importance, as the variability of floods directly affects life and human activities. This study examines the fluctuations and persistence of winter floods in 14 catchments in the Rika River Basin (Ukraine) and ten catchments in the Steyr River Basin (Austria). The catchments represent typical hydrological regimes in the Danube River region. The fluctuations and persistence of floods are analyzed by the hydro-genetic method and a seasonality analysis for the period 1951–2015. The results show a much more pronounced fluctuation pattern in the upper Rika catchments than in the upper Steyr catchments. This pattern indicates an increase in winter flood magnitudes between the mid-1960s and the 1990s, followed by a decrease until recently. The flood seasonality shows a large inter-annual variability in both regions. The most significant winter floods tend to occur in November and December. The winter flood fluctuations are compared with changes in associated climate characteristics, i.e., seven-day maximum precipitation, a melt index, and annual maximum snow depth. The seasonality of these characteristics has a strong inter-annual variability and only partly explains the winter flood fluctuations.