Understanding flood variability in the European Alps is critical for risk management, yet causal mechanisms linking climate drivers to floods remain unclear. Previous studies have largely relied on correlations, limiting causal attribution. Here we apply a constraint-based causal inference framework using the PC-stable algorithm, combined with bootstrap stability analysis and Granger causality validation, to multi-centennial climate and flood proxy records from the Hasli-Aare catchment (1300–2020 CE). Our results reveal that total solar irradiance modulates summer atmospheric circulation, notably the summer North Atlantic Oscillation, which causally influences alpine flood frequency. These relationships are strongest during the preindustrial period and weaken under modern anthropogenic forcing, indicating a shift in dominant flood drivers. Our study demonstrates the utility of causal inference methods in paleoclimate research and offers a framework for investigating changes in the drivers of hydrological extremes, important for climate attribution and risk assessment in mountain environments.