Objective Agricultural sustainable development and aquatic ecological environment security are faced with numerous challenges. As a non-renewable resource, phosphorus (P) is an essential element for crop growth, but has the potential to cause water eutrophication. Disparities in P management such as fertilizer or manure and the harvested crop P removal result in a massive variation of P imbalances in agricultural systems. Phosphorus loss is mainly affected by the form and availability of soil P.Method Therefore, in this paper, considering strong spatial differentiation characteristics of soil P pools and availability, the soils of typical flood and drought rotation farmlands were selected. The farmlands were located in the Taihu Lake Region in the lower reaches of the Yangtze River. In detail, 319 farmland soil samples and 83 wheat samples were collected based on the systematic random point distribution method. The spatial differences of soil phosphorus fractionations and crop P uptake were analyzed.Result Compared with the results of the second national soil survey and the survey in 2009, soil total P (TP) and available P(Olsen-P)increased significantly in the Taihu Lake Region. Soil Olsen-P concentration in Changshu and Yixing city ranged between 2.19-112.5 mg·kg^–1 and 5.21-109.7 mg·kg^–1, respectively. The average concentration was 37.6 mg·kg^–1 and 29.8 mg·kg^–1, which increased by 24.6 mg·kg^–1 and 7.9 mg·kg^–1 _--in contrast to 2009. The concentration of available P exceeded 10 mg·kg^–1 of 93.1% of soil samples, and 65.2% of the total soil samples had more than 20 mg·kg^–1, which indicated that most of the paddy soil P pool was in surplus. Furthermore, we analyzed soil P availability using the biologically-based P (BBP) method, and found that CaCl₂-P, Citrate-P, Enzyme -P and HCl-P had a significant positive correlation with Olsen-P (P < 0.001). This indicates that those four P forms were all available sources of soil P. We also found a notable relationship between soil TP and Olsen-P (P < 0.001) or crop TP (P < 0.01) concentration. Meanwhile, the correlation analysis of CaCl₂-P and Olsen-P indicated the breakpoint of environmental risk, which was 30 mg·kg^–1.Conclusion In view of the strong spatial differences of soil phosphorus pools in this region, it is suggested to focus on the efficient utilization of soil phosphorus in the regional nutrient management and environmental protection. The results are expected to provide basic data support for increasing P use efficiency as well as agricultural non-point source pollution control in the Taihu Lake Region.