Lagoons, significant coastal wetlands, stand out for their vital role in the cycles and transformations of phosphorus. However, the relationship between the spatial distributions of various phosphorus forms in the soil and sediments of lagoon areas remains unclear. This study investigated the phosphorus fractions and distribution patterns in the soil and sediments from Shimei Inland Sea, Hainan Province, China, and identified the factors controlling phosphorus distribution and its relationship with lagoon eutrophication. The results revealed significant enrichment of inorganic phosphorus (IP) in the Shimei Inland Sea (64.1–679.0 mg/kg) and offshore areas (56–627.2 mg/kg), while organic phosphorus (OP) was relatively concentrated in land (60–744.3 mg/kg), suggesting that the productivity of the terrestrial ecosystem controlled the OP content and IP formed from the mineralization of OP was more likely to leach into the water and combine with minerals. Total phosphorus (TP) content was negatively affected by pH, and organic matter, cation exchange capacity and iron/aluminum oxides showed significant positive correlations with TP content. These findings highlighted the coupled impact of soil and sediment physicochemical properties on phosphorus enrichment and transformation, providing theoretical support for the ecological restoration of ecosystems in tropical coastal wetlands.