The Guapimirim estuary is the main tributary of Guanabara bay and is located in the northeast portion. Although it is protected, this estuary has been experiencing strong anthropogenic pressure, which has led to changes in the natural characteristics. Large amounts of sewage are dumped into the bay through tributaries, thereby changing the water and bottom sediment quality. One of the main elements of sewage is phosphorus. Despite its importance to life, a high concentration of this nutrient in the environment can result in eutrophication. This work describes the phosphorus distribution in its different fractions in the bottom sediment at 16 stations located in the main channel of the Guapimirim estuary. These results are correlated with data on grain size, organic matter and calcium carbonate content in the bottom sediment and with physicochemical parameters of the bottom water. The grain size decreases toward the mouth of the estuary, whereas the organic matter and carbonate content increase. The salinity increases significantly at 3.5 km upstream from the mouth, where there is also a notable increase in fine sediments; the same site is the mean position of the salinity front. The temperature and pH increase in the same direction. The Pinorg-total ranges between 3.18 and 7.13 µmol g−1, increasing toward the mouth. The same trend is observed for the other phosphorus fractions P-Ca, P-Fe and P-f.a., which range from 0.68 to 1.91, 0.79 to 1.71 and 0.03 to 0.93 µmol g−1, respectively. The P-Ca and P-Fe fractions are the most representative in the Pinorg-total, occurring at 26.3 and 26.0 %, respectively.