Few of the large Southern peri-alpine lakes have been studied with a sedimentological approach in their deep basin to understand the dynamics of their long-term sedimentation due, among other factors, to the high complexity of the coring in such deep lakes. In 2018, a 15.5 m-long sediment section was retrieved from the deep basin of Lake Iseo (Italy) at 251 m of water depth. Seismic survey associated to a multi-proxy approach with sedimentological and geochemical analyses, reveals a high number of event layers that corresponds to 61.4 % of the total sedimentation during the last 2000 years. The great heterogeneity of textures, colours, and grain-size distribution between the different types of event layers can be explained by the high number of potential sources of sediment inputs in this large lake system. By combining proxies for sediment source with transport processes, we were able to distinguish: i) flood events, and ii) destabilisations of slopes and deltas due to an increase of the sediment load and/or to seismic shaking. From a thorough comparison with both, the regional climatic fluctuations, and the human activity in the watershed, it appears that periods of high sediment remobilization can be linked to a previous increase in Critical Zone erosion in the watershed mainly under human forcing. Hence, even in large catchments, human activities play a key role on erosion processes and on sediment availability, disrupting the recording of the Critical Zone functioning in such lacustrine archive.