Sediment phosphorus (P) diagenesis and release in polymictic systems are poorly understood. Here, we determine the mechanistic controls on the processes that drive P release from the sediments in Lake of the Woods (LOW). The vertical distributions of the relevant diagenetic parameters—including oxygen, pH, redox potential, dissolved P, iron (Fe) and other metals in the porewater—were measured, and the fluxes of dissolved oxygen and P across the sediment-water interface (SWI) at the four locations in LOW were quantified. We characterized solid P speciation and analyzed the iron and corresponding metal contents in five sediment P binding forms. Short-term diffusive fluxes of P ranged between 0.3 and 7.8 mg m−2d−1, controlled by the mineralization of freshly deposited organic matter and the redox-sensitive iron cycle. Long-term net P release rates were between 0.21 and 9.96 mg m−2d−1, controlled by the diagenetic remineralization of P binding pools, which regulates long-term sediment P releases. Hypoxia may have led to the release of previously stored FeP in the sediments, which has likely increased internal P loading for a timescale that is longer than seasonal. While Fe-sorbed phosphorus is the major barrier for P release in the surface sediments, P is immobilized in deep sediments via the formation of calcium (Ca)-P, aluminum (Al)-P, and possibly vivianite. Our study demonstrates the importance of sediments as sources of the productivity-limiting nutrient phosphorus; reveals the geochemical controls on sediment P release; and helps further the understanding of how sediments regulate water quality and affect eutrophication and the possibility of algal blooms.