Phosphorus (P) forms, with respect to sediment characteristics, and an in-stream sluice were studied in the river–lake system, Huai River catchment area, China. The mean of total P in sediments in the mainstream of the Huai River was higher than that in the Hongze Lake. It was found that P fractions varied in the sediments throughout the river and lake. Detrital-P was the dominant P fraction in the mainstream and organic P and detrital-P were the dominant P fractions in the lake, which could indicate: biologically available and non-biologically available forms. Useful information for the interpretation of P fractions could also be obtained from major sediment characteristics. Whether the relations between P fractions and grain size characteristics were significant or weak, 0.125 mm was a threshold grain size for P fraction distribution in sediment. In addition, the Bengbu Sluice, one of the most important in-stream facilities in the Huai River catchment area, regulated not only the transport of P in sediments upstream and downstream of the sluice, but also the distribution of P fractions in the river–lake system. Therefore, it was confirmed that nutrient loadings could be prevented from reaching the watershed, as well as improved ecological diversity by integrating sluice operation.