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The effects of phosphorus (P) fertilizer on P loss potential, soil Olsen-P and neutral phosphatase activities in paddy soils fertilized with superphosphate or pig manure (PM) were evaluated in this paper. Data were collected from a field experiment in the Tai Lake Basin, China. Superphosphate rates were 0, 17.5, 26.7, and 35.0 kg P/ha, and PM rates were 0, 1.4, 2.1, and 2.8 t/ha for each crop, respectively. Soil Olsen-P in the plow layer increased to a greater extent with PM than with superphosphate. Pig manure increased neutral phosphatase activities in the plow layer compared with PM-free treatment. In contrast, superphosphate inhibited neutral phosphatase activities compared with superphosphate-free treatment. Spring application of P fertilizer markedly increased the total P of surface water in November (< 0.01 vs. 0.10 mg/L) compared with P-free treatment. The total P of shallow groundwater at a 75 cm depth was ~0.01 mg/L. Phosphorus fertilizer did not influence Olsen-P or neutral phosphatase activities under the plow layer. Downward movement of P did not occur. Appropriate rate of P application of 26.2 kg P/ha for each crop in this soil reduced the risk of P loss in the paddy wetland ecosystem.