In recent decades, there have been discussions and predictions regarding the impact of climate on floods, due to its socioeconomic and environmental consequences. For accurate prediction of future flood events and their impacts, it is crucial to have an improved understanding on past flood events. Lacustrine sediments have been used as a natural archive to study the past flood events. Here, we study the impact of 1954 flood event on the lacustrine environment of Bengas and Rupa Lake in central Nepal based on X-ray fluorescence spectrometry (XRF) element analysis, magnetic susceptibility (MS), total organic carbon (TOC) and the biomarker molecular compositions. Results showed that 1954 flood event had significant impacts on the two lakes in terms of detrital input, organic matter deposition and aquatic production. Before the flood event, both two studied lakes had relatively lower catchment erosion rate, lower organic matter deposition and aquatic production. During the flood event, catchment erosion and aquatic production increased in both lakes due to mass transport deposits and the increased nutrition loading attributed to flood event. Following the flood event, Begnas Lake showed the sharp increase in organic matter deposition, whereas in the Rupa Lake organic matter deposition showed minor changes. The difference in organic matter deposition in lakes during flooding event is likely due to detrital material brought and deposited by the flood activity. Overall our results suggest that lacustrine sediments are sensitive to the extreme event and would be an ideal archive for the reconstruction of flood events.