This dataset presents multi-proxy records from four sediment cores (LV1-LV4) collected in Lake Victoria, spanning the past 17 kyr. Core sites range from 13.4 to 63 m water depth, capturing spatial and environmental variability in the past. The dataset integrates non-desctructive analyses X-ray fluorescence (XRF), hyperspectral imaging (HSI) with biogeochemical data (e.g., TOC, TN, bSi, δ13C, δ15N, sedimentary pigments).