It is widely acknowledged that dams affect sediment transport and water quality. To support water management of reservoirs, it is useful to explore how the fractions of phosphorus (P) in sediments were changed after the dam was built. The aim of this study was to assess the spatial and temporal trends of the P fractions in sediments from the Miyun Reservoir, a pivotal drinking water supply for Beijing City, the capital of China. Nine surface sediment samples, together with a sediment core, were collected. The concentrations of total P (TP) and their fractions were then determined by using a sequential extraction method. The results showed that the reservoir was classified into three areas spatially based on the TP concentrations, i.e., high (Baihe area), medium (transitional area), and low (Chaohe area) concentrations. The concentrations of iron-bound P (BD-P) and metal oxide–bound P (NaOH-P) were higher in the Baihe and Chaohe regions than those in the transitional area and tended to increase with water depth. Dam construction can lead to the concentrations of P increased in sediments and further increase the potential of internal P loadings. This study revealed the effect of dam construction on sedimentary P accumulation. The results will be helpful in better understanding the mobility and bioavailability of P in the aquatic ecosystem, which aim to achieve a more highly targeted environmental management for this important region.