The nutrient content in soil surface water indicate the nutrient levels in soil and could be used to estimate nutrient loss and its environmental effects. Study of the nutrient dynamics in soil surface water under fertilization provides fundamental information for optiming fertilization practices. In order to investigate the responses of N and P in surface water of paddy soils to different rates of swine manure application, a pot experiment was conducted by using double-rice amended with eight rates of swine manure from 0–44.8 t/hm2, and nutrient contents were measured periodically. Results showed that the average contents of total P, total N, ammonium N and organic N in surface water in early rice season ranged from 0.04–1.13, 3.17–12.97, 1.81–5.11 and 1.17–7.39 mg/L, respectively. The contents increased in late rice season and ranged from 0.13–7.98, 3.17–25.57, 1.21–10.41 and 1.87–15.35 mg/L, respectively, in which total P was prone to accumulate with a maximum increase of 6 folds compared to the early rice season. The nutrient content correlated linearly (P<0.001) with the application rate, and increased significantly when the application rate reached 11.2 t/hm2. The nutrient content reached its peak in the first 4 d and 14 d after manure application. Compared with chemical fertilizer, the amendment of swine manure resulted in the domination of organic nitrogen, which can account for 66% of the total nutrient in surface water, and extended the intensive nutrient releasing period for one week. The accumulation effect suggests that consecutive application of swine manure at high rate could result in the saturation of the nutrient preserving capacity of soil, thus increasing the risk of nutrient loss. Therefore, attention should be paid to the combined effects of both application rate and frequency.