The dataset reports sediment data obtained from a three-year sediment trapping (2011-2013 CE) at two locations (proximal and distal towards the river inflow) in Lake Mondsee, Austria in comparison to a varved surface sediment core (1986-2013 CE) from the distal location and river runoff. The sediment trap data includes stable oxygen and carbon isotope composition, sediment flux and carbon contents, the sediment core data includses stable oxygen and carbon isotope composition of seasonal calcite layers and bulk samples and the thickness of detrital layers.