<p>Agricultural and mining activities in northern Tunisia greatly influence water resource management policies, with the Sidi Salem Dam, the largest in the country, being a key component. The concentration profiles and diffusion fluxes of PO₄³⁻, NH₄⁺ and NO₃⁻ at the water–sediment interface, along with the chemical speciation of phosphorus and heavy metals (Pb, Zn, Cu, Cd, and Cr), were analyzed in three sediment cores from the Sidi Salem Dam Lake. The results show that phosphorus in the sediment is associated with carbonates (P-Ca 40 to 60%) and iron from 0 to 10 cm depth (P-Fe 25–30%). This association seems to be related to pH regarding P-Ca and Eh regarding P-Fe. The PO₄³⁻ and NH₄⁺ fluxes are either zero or directed toward the water column (7–16 µmol m⁻² d⁻¹) for NH₄⁺, except NO₃⁻, whose flux at the dam entrance is directed toward the sediment (− 8.44 µmol m⁻² d⁻¹). Cd contents are negligible in all cores; Zn and Cr are highest in the three studied sites; and Pb and Cu are mainly high at the dam entrance (20–43.7 µg g⁻¹ at 10 cm depth for Pb). Chemical fractionation shows that Pb, Zn, Cu, and Cr are mainly associated with the residual phase (41%, 71%, 53%, and 95%). These results highlight the relevance of suboxic environments and geochemical interactions in regulating nutrient and metal fluxes. While phosphorus mobility is especially sensitive to pH and redox dynamics, trace metal pollution does not systematically indicate toxicity, providing a more nuanced view of environmental management in watersheds affected by mining.</p>