Inappropriate organic fertilizer application may cause serious environmental risks, especially nitrogen (N) and phosphorus (P) losses. To achieve a win–win for high yield and environmental protection in organic agriculture, it was essential to demonstrate the relationship between the organic fertilizer input, rice yields, and risks of N and P losses. Based on a rice and green manure cropping rotation field experiment in the Yangtze River Delta of China, the effects of organic fertilization rates on the dynamics of surface water N and P concentrations and rice grain yields were determined. The results showed that the N (total N, ammonium-nitrogen, nitrate-nitrogen) and P (total P and dissolved P) concentrations in surface water immediately and greatly reached the highest values 1 day after basal fertilization and topdressing fertilization. Then, the N and P concentrations sharply decreased and were maintained at a relatively low level. The initial 3 and 7 days after organic fertilization were the high-risk periods for controlling N and P runoff losses. The surface water N and P concentrations had a positive correlation with the organic fertilization rate in high-risk periods. Besides, the effects of organic fertilization on surface water P concentrations existed longer than those of N concentrations. The rice grain yields increased with the increase in organic fertilization rates, but high organic fertilizer input (>225 kg N per hectare) did not increase the grain yield. Meanwhile, the high organic fertilizer input had the highest risks for N and P losses. Therefore, in organic rice farming, organic fertilization rates with 150~200 kg N per hectare are the optimal organic fertilizer input, with relatively high grain yields and low N and P losses.