Soil erosion and associated sediment transfer are among the major causes of aquatic ecosystem and surface water quality impairment. Through land-use and agricultural practices, human activities modify the soil erosive risk and the catchment connectivity, becoming a key factor of sediment dynamics. Hence, restoration and management plans of water bodies can only be efficient if the sediment sources and the proportion attributable to different land-uses are identified. To this aim, we applied two approaches, namely compound-specific isotope analysis (CSIA) of long-chain fatty acids (FA) and triterpenoid biomarker analysis, to the eutrophic Lake Baldegg and its agriculturally used catchment (Switzerland). Soils reflecting the five main land-uses of the catchment (arable lands, temporary and permanent grasslands, mixed forests, orchards) were subjected to CSIA. The compound-specific stable isotope δ 13 C signatures clearly discriminate between grasslands (permanent and temporary) and forests. Signatures of agricultural land and orchards fall in-between. The soil signal was then compared to the isotopic signature of a lake sediment sequence covering ca. 130 years (before 1885 to 2009). Most of the lake sediment samples lie out of the source soils polygon, most likely as a result of carbon exchanges with highly depleted material related to methanotrophic bacterial activity. The recent lake samples falling into the soil polygon indicate an important contribution of the forests, which can be explained by (1) the location of the forests on steep slopes, resulting in a higher connectivity of the forests to the lake, and (2) potential direct inputs of trees and shrubs growing along the rivers feeding the lake and around the lake. Despite the strong bacterial overprint on the isotopic signal, land-use and catchment history are clearly reflected in the CSIA results, with isotopic shifts being consistent with catchment, land-use and eutrophication history. While present in the soils, the investigated highly specific biomarkers were not detected in the lake sediment. Two trimethyltetrahydrochrysenes (TTHCs), natural diagenetic products of pentacyclic triterpenoids, were found in the lake sediments. Their origin is attributed to the in-situ microbial degradation of some of the triterpenoids. While the need to apportion sediment sources is especially crucial in eutrophic systems, our study stresses the importance of using caution with CSIA and triterpenoid biomarkers in such environments, where the presence of methanotrophic bacterial biomass might overprint original isotopic signals.