Freshwater sediments are important carbon reservoirs, but the extent to which different components of soil or aquatic organic matter (OM) are deposited in these sediments is not well defined. Bulk sediment carbon (δ13C) and nitrogen (δ15N) stable isotope ratios, as well as radiocarbon, are valuable tracers for sediment OM sources, but there are few studies comparing the isotopic composition of soil and sediment OM at the catchment scale. We analyzed spatial variation in δ13C, δ15N, 14C, and C:N ratios in OM from soils, stream and lake sediments, and aquatic plants and algae, in a temperate forest lake catchment in southern Quebec, and used a Bayesian model to estimate source mixtures for sediment OM. Sediments at the stream mouths entering the lake were characterized by high C:N ratios, high fraction modern carbon (Fm), and low δ13C, indicating preferential deposition of plant-derived OM. In contrast, sediments sampled further upstream during a period of low streamflow indicated a larger proportion of microbial OM based on low C:N ratios and high δ15N. In lake sediments we observed zonation of OM isotopic composition by water depth. Shallow sediments (0–1 m water depth) were characterized by high amounts of plant-derived OM, while intermediate-depth sediments (1–3 m) were characterized by high δ13C, indicating an increased input of OM from aquatic plants. Deep lake sediments (> 4 m) were characterized by low δ13C and Fm values, which likely reflect greater input of phytoplankton OM. Stream sediments downstream of the lake exhibited high δ15N and low Fm values, implying a greater input of aged microbial biomass from soils. Our results indicate catchment-scale spatial differentiation in the source of OM in sediments, with zones of preferential deposition of terrestrial plant, aquatic plant, phytoplankton, and soil microbial biomass.