Lake Victoria situated in East Africa faces an acute problem with eutrophication. Many reasons like agricultural production, industrialization, anthropogenic processes, the introduction of species, and economic activities have caused a stress to the overall well-being of the lake. Excess carbon, nitrogen, and phosphorus drive an increase in productivity which affects eutrophication. Previous studies on sediments and nutrient concentrations in the lake have concluded that nutrient concentrations increase due to release from the catchment. This study focuses on catchment sediments collected from four different sites and compares the results with sediments from two additional sites in the lake. The sediment core from Siaya indicates the highest concentrations of TOC (180 g/kg), TN (13 g/kg) and TP (17000μg/L). It is a rural site and poor agricultural practices such as the burn and slash, use of too many fertilizers, clearance of land, atmospheric deposition and precipitation increase elemental concentrations in the sediments compared to the more urban sites. In the lake sediments, the BILL core had higher concentrations of TP (430g/kg) and TN (16 g/kg) compared to the other site (LV-95) which is located far away from the margins of the lake. This core, however, had high TOC levels (180g/kg). The increase of nutrient levels in lake sediments is thought to be due to non-point sources from the catchment. Analyses of stable carbon isotope were used to infer the different organic matter source in the sediments. Based on the range of values for δ13C vs. C/N it is inferred that aquatic algal production and C4 vascular plants are the dominant sources for the organic matter input. The chemical characterization of catchment and lake sediments provides a qualitative link to nutrient influx and eutrophication in the lake.