Severe floods triggered by intense precipitation are among the most destructive natural hazards in Alpine environments, frequently causing large financial and societal damage. Potential enhanced flood occurrence due to global climate change would thus increase threat to settlements, infrastructure, and human lives in the affected regions. Yet, projections of intense precipitation exhibit major uncertainties and robust reconstructions of Alpine floods are limited to the instrumental and historical period. Here we present a 2500-year long flood reconstruction for the European Alps, based on dated sedimentary flood deposits from ten lakes in Switzerland. We show that periods with high flood frequency coincide with cool summer temperatures. This wet-cold synchronism suggests enhanced flood occurrence to be triggered by latitudinal shifts of Atlantic and Mediterranean storm tracks. This paleoclimatic perspective reveals natural analogues for varying climate conditions, and thus can contribute to a better understanding and improved projections of weather extremes under climate change.