Sediments of alpine lakes serve as crucial records that reveal the history of lacustrine basins, offering valuable insights into the effects of global changes. One significant effect is the variation in rainfall regimes, which can substantially influence nutrient loads and sedimentation rates in lacustrine ecosystems, thereby playing a pivotal role in shaping biotic communities. In this study, we analyze subfossil chironomid assemblages within a sediment core from an alpine lake (western Italian Alps) to investigate the effects of rainfall and flood regime variations over the past 1200 years. Sediment characterization results highlight changes in sediment textures and C/N ratio values, indicating phases of major material influx from the surrounding landscape into the lake basin. These influxes are likely associated with intense flooding events linked to heavy rainfall periods over time. Flooding events are reflected in changes in chironomid assemblages, which in our samples are primarily related to variations in sediment texture and nutrient loads from the surrounding landscape. Increased abundances of certain taxa (i.e., Brillia, Chaetocladius, Cricotopus, Psectrocladius, Cricotopus/Orthocladius Parorthocladius) may be linked to higher organic matter and vegetation inputs from the surrounding landscape. Biodiversity decreased during certain periods along the core profile due to intense flood regimes and extreme events. These results contribute to our understanding of alpine lake system dynamics, particularly those associated with intense flooding events, which are still understudied.