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. According to this aim, we applied two approaches, namely compound-specific isotope analysis (CSIA) of long-chain fatty acids (FAs) and triterpenoid biomarker analysis, to a eutrophic lake, 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 δ¹³C signatures clearly discriminate between potential grasslands (permanent and temporary) and forest sources. Signatures of agricultural land and orchards fall in between. The soil signal was compared to the isotopic signature of a lake sediment sequence covering ca. 130 years (before 1885 to 2009). The recent lake samples (1940 to 2009, with the exception of 1964 to 1972) fall into the soil isotopic signature polygon and indicate an important contribution of the forests, which might be explained by (1) the location of the forests on steep slopes, resulting in a higher connectivity of the forests to the lake, and/or (2) potential direct inputs of trees and shrubs growing along the rivers feeding the lake and around the lake. However, the lake sediment samples older than 1940 lie outside the source soils' polygon, as a result of FA contribution from a not yet identified source, most likely produced by an in situ aquatic source, either algae, bacteria or other microorganisms or an ex-site historic source from wetland soils and plants (e.g. Sphagnum species). Despite the overprint of the yet unknown source on the historic isotopic signal of the lake sediments, land use and catchment history are clearly reflected in the CSIA results, with isotopic shifts being synchronous with changes in the catchment, land use and eutrophication history. The investigated highly specific biomarkers were not detected in the lake sediment, even though they were present in the soils. However, 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 exercising caution with CSIA and triterpenoid biomarkers in such environments, where the active metabolism of bacteria might mask the original terrestrial isotopic signals.