Nutrients released from sediments have a significant influence on the water quality in eutrophic lakes and reservoirs. To clarify the internal nutrient load and provide reference for eutrophication control in Yuqiao Reservoir, a drinking water source reservoir in China, pore water profiles and sediment core incubation experiments were conducted. The nutrients in the water (soluble reactive P (SRP), nitrate-N (NO3−-N), nitrite-N (NO2−-N), and ammonium-N (NH4+-N)) and in the sediments (total N (TN), total P (TP) and total organic carbon (TOC)) were quantified. The results show that NH4+-N was the main component of inorganic N in the pore water. NH4+-N and SRP were higher in the pore water than in the overlying water, and the concentration gradient indicated a diffusion potential from the sediment to the overlying water. The NH4+-N, NO3−-N, and SRP fluxes showed significant differences amongst the seasons. The NH4+-N and SRP fluxes were significantly higher in the summer than in other seasons, while NO3−-N was higher in the autumn. The sediment generally acted as a source of NH4+-N and SRP and as a sink for NO3−-N and NO2−-N. The sediments release 1133.15 and 92.46 tons of N and P, respectively, to the overlying water each year.