Lake sediments are a potential source of mercury (Hg) for aquatic biota. Here, we investigated the predictive power of (a) key parameters for lake catchment morphometry and (b) organic matter composition of sediments in an effort to account for observed variations of total (THg) and methyl (MeHg) mercury concentrations in lake sediments. Using regression models we demonstrate that the morphometric parameters lake depth as well as inclination of catchment soils and lake bottoms can significantly predict variations of THg concentrations, but not MeHg, at profundal lake sediments. Although THg and MeHg concentrations in sediments could not be predicted by specific organic matter sources, as elucidated by atomic C/N ratios, our data suggest that wetland-derived total organic carbon (TOC) contained less THg concentrations than TOC derived from mostly forested watersheds. However, TOC concentrations could significantly predict MeHg concentrations and the proportion of methylated Hg at all sediment stations. Finally, from an ecotoxicological point of view, we propose that concentrations of TOC at surface lake sediments, rather than parameters of catchment morphometry, may predict dietary sources of MeHg for benthic consumers and consequently perhaps for organisms at higher trophic levels.