Climate change may systematically impact hydro-meteorological processes and their interactions, resulting in changes in flooding mechanisms. Identifying such changes is important for flood forecasting and projection. Currently, there is a lack of observational evidence regarding trends in flooding mechanisms in Europe, which requires reliable methods to disentangle emerging patterns from the complex interactions between flood drivers. By using a novel explainable machine learning framework, combined with cluster analysis, we identify three primary patterns that drive 55,828 annual maximum discharge events in over a thousand European catchments. The patterns can be associated with three catchment-wide river flooding mechanisms: recent precipitation, antecedent precipitation (i.e., excessive soil moisture), and snowmelt. The results indicate that over half of the studied catchments are controlled by a combination of the above mechanisms, especially recent precipitation in combination with excessive soil moisture, which is the dominant mechanism in one-third of the catchments. Over the past 70 years, significant changes in the dominant flooding mechanisms have been detected within a number of European catchments. Generally, the number of snowmelt-induced floods has decreased significantly whereas floods driven by recent precipitation have increased. The detected changes in flooding mechanisms are consistent with the expected climate change responses, and we highlight the risks associated with the resulting impact on flooding seasonality and magnitude. Overall, the study demonstrates the important role of explainable machine learning in uncovering complex and possibly non-linear changes in weather and climate extremes events and their drivers under climate change.