Phosphorus (P) in agricultural soils is an important factor for soil quality and environmental protection. Understanding of P and its fractions in soils on a regional scale is imperative for effective management or utilization of P and the improvement of P availability in soils. To study spatial variability and changes of soil P and its fractions as affected by farming practices, soil samples were taken in Rugao County, Jiangsu Province of China, an intensive agricultural area in the Yangtze River Delta region, in years of 1982 (n = 1 514), 1997 (n = 1 651), and 2002 (n = 342). High spatial variabilities of Olsen P and total P (TP) were observed throughout the study area. Loamy Stagnic Anthrosols and clay or loamy Aquic Cambosols had significantly higher concentrations of Olsen P and TP than sandy Ustic Cambosols and Aquic Cambosols. Olsen P and TP were increased from 1982 to 2002. The accumulations of Olsen P and TP in the cultivated soils were likely related to the increased application of P fertilizer, organic input, and soil incorporation of crop residues as well as conversion of soil use. Accumulated soil P was dominantly in labile and semi-labile P fractions. These P fractions may be utilized by future crop production by adjusting management practices, but they also pose a serious threat to nearby water bodies. Future strategies should include decreasing P fertilization in soils and supporting sustainable management. The information from this study can be used to monitor changes in soil fertility and environmental risks so that the use of fertilizers can become more rational.