Bioavailable P-forms in Bizerte lagoon and the adjacent open waters of the north-eastern Mediterranean, were quantified with the SEDEX sequential extraction method. Pore water analysis, sediment total organic carbon and the mineralogical composition of sediment samples were also determined and potential P release at the lagoon’s water-sediment interface was assessed through benthic chamber experiments. Sediment shows an abundance of quartz and calcite in different core samples from the lagoon center, while pyrite is observed in samples from the open sea. Relative abundance of Fe-bound phosphorus in the sediments reveals the co-precipitation of both constituents as P-containing iron (oxyhydr) oxides. Phosphorus bioavailability was greater in the lagoon than in the open sea, dependent on Ca–P fractionation, and promoting P sediment immobilization. Pyrite presence is related to periodic anoxic events inducing P release upwards in relation to periodic increases in organic loads.