The Anllóns basin (NW Spain) has been included in the Natura 2000 Network and declared as Site of Community Importance. The main contamination problems of the basin come from a former gold mine and from agricultural activities, which influence the quality of the sediment-water system. Phosphorus (P) enrichment in the bed sediments was evaluated by analyzing P in the pore waters, in the surface bed sediments, and in the vertical sediment profiles, including both total and bioavailable forms. Two granulometric fractions (<2 mm and <63 μm) were evaluated. Pore waters, bed sediments, and vertical profiles showed high percentages of the bioavailable P fraction with respect to the total P content, which evidences the potential risk of pollution which suppose the bed sediments of the Anllóns River. The vertical profiles showed P enrichment in the superficial layers, which could be the consequence of the increased use of fertilizers in the last decades. With regards to the granulometric distributions, the <63 μm showed, in general, higher P concentrations than the <2 mm fraction. However, at the sampling points most heavily contaminated, the concentration of both fractions becomes similar, thus indicating that, at these sites, the coatings formed over sands can retain important P concentrations in the bed sediments.