High phosphorus (P) concentrations in the run-off from farmlands facilitate the displacement of native vegetation by undesirable vegetation. Everglades restoration, as well as sustainable crop production, requires major reductions of P in runoff, and this requires in-depth knowledge of P biogeochemistry in soils. We conducted a series of laboratory, greenhouse and field experiments on P chemistry (sorption, precipitation, fractionation, leaching, etc.) and P fertilizer use efficiency in calcareous gravelly and marl soils. We found that most agricultural soils have high concentrations of P in forms likely to move into surface and groundwater even under calcareous conditions, and that additional applications of P fertilizer did not increase P availability and crop yield. We developed a simple one-point isotherm method to predict saturation and leaching potential of P in calcareous soils. We found apatite (phosphate mineral) formed in calcareous soils farmed for many years, which has little impact on natural ecosystems. The Best Management Practices (BMPs) should be implemented for crop production and various storm water treatment technology can be used to removal P from agricultural runoff.