The quality of aquatic ecosystems can be significantly impacted by the input of nutrients and trace elements. Identifying the sources and bioavailability of these components is crucial for understanding their cycling and assessing the environmental effects in lakes subjected to increased anthropogenic pressure, such as Lake Paranoá, a man-made reservoir in Brasília, Brazil. This study explores the spatial distribution and geochemical partitioning of sedimentary nutrients and metals in Lago Paranoá, aiming to pinpoint their origins and behaviors. The sediment distribution patterns in Lago Paranoá reflect the lake’s hydrodynamics, including water currents and proximity to material sources. Human-induced erosion due to urban expansion contributes to the influx of terrigenous and anthropogenic compounds into the lake. Our findings indicate that Ca, Mg, P, and Zn are associated with anthropogenic sources, likely from domestic sewage discharge and/or leaching from construction activities. Notably, sediments near the Wastewater Treatment Plant (WWTP) show elevated concentrations of P, Ca, Mg, and Zn, identifying the WWTP as a key source. Additionally, the high levels of P, Mn, and Zn in weakly acidic phases suggest these elements may readily desorb from sediments, potentially migrating into the water column during early diagenetic processes. This study provides essential insights for evaluating the potential impacts of the upcoming sediment dredging project in Lago Paranoá.