Shahe Reservoir in the headwater of the Wenyu River, Beijing City, was selected for a case study evaluating the effects of both urbanization and agricultural intensification on the cycling of phosphorus (P), as well as Cr, Cu, and Ni. This study showed that the construction of the reservoir in 1960 resulted in an increased retention of P, Cr, Cu, and Ni in its sediment. The load of these elements to the river system has sharply increased since the 1980s. For P, the mean sediment content was 890 ± 270 mg/kg before 1980, but thereafter increased to 1540 ± 700 mg/kg. Most of the sedimentary P was apatite P (47%). The average sediment contents of Cu and Ni increased from 37.3 and 28.8 g/kg to 61.6 and 60.7 mg/kg, respectively. According to mass balance calculations, the actual annual input loads were 110 t P, 500 kg Cr, 520 kg Cu, and 600 kg Ni. Whereas the reservoir retained about 50% of the trace metal loads in its sediment, P retention was only 7%. Hence, the sediment contribution to the P balance of the reservoir is almost negligible and sediment manipulation cannot be a measure for the mitigation of eutrophication in this reservoir.