Phosphorus (P) is a major nutrient for plant growth, and it is often the primary limiting nutrient in freshwater ecosystems controlling algal blooms. The Bronx River of New York City, New York, USA includes freshwater and coastal water systems. The water quality of both fresh and saline water is lower than the standard levels designated by New York State, and classified as Class B and Class I waters, respectively. Algal blooms and oxygen depletion within the river have degraded the water quality, endangered fishing, and limited recreational use. The internal loading of P, an important bioavailability indicator in the Bronx River, is determined by the sorption processes, i.e., cycling of P between solid and liquid phases. The objectives of this study were to understand how P sorption characteristics affect the internal loading of P and the conditions that might give rise to a flux of P from sediment to the water column, and to estimate the effects of physicochemical properties of the sediments on P sorption parameters. Bed sediments were collected from 15 sites along the Bronx River, from the origin in Westchester Davis Brook, Kensico Dam through the Bronx to the Sound View Park estuary. Phosphorus sorption maximum (S(max)) were significantly correlated with oxalate-extractable iron (Ox-Fe) and aluminum (Ox-Al), acid-extractable calcium (HCl-Ca) and magnesium (HCl-Mg), and total organic matter (OM), suggesting that not only metal ions affected P sorption characteristics, but OM also influenced the P sorption processes. This study also showed that originally sorbed P (S(0)) was significantly correlated with Ox-Fe, Ox-Al, HCl-Mg, and OM. The extremely high values of the percentage of sorbed P retained in sediments (>98% for all sites except the two estuary sites: site 13 of 88% and site 14 of 92%) suggest that a large flux of P to the water column from the sediments could potentially occur under changing hydro-climatic conditions, such as the changes in pH, ionic strength and redox conditions, which may, in turn, exacerbate eutrophic conditions and subsequent algal blooms.