Changes in snow affect the runoff seasonality, including summer low flows. Here we analyse this effect in 59 mountain catchments in Czechia. We show that snow is more effective in generating runoff compared to rain. Snow-poor years generated lower groundwater recharge than snow-rich years, which resulted in higher deficit volumes in summer. The lower recharge and runoff in the case of a snowfall-to-rain transition due to air temperature increase might be critical for water supply in the future.