Mangrove sediments in the South China Sea, particularly in the Hainan Island region, play a crucial role in regulating heavy metal migration and sequestration. However, the impact of converting mangrove areas to fish and shrimp culture ponds on heavy metal pollution in the Bamen Bay Mangrove Reserve is unclear. This study evaluates the pollution levels and ecological risks of Cr, Zn, Pb, Cu, and As in sediments from three land-use types using pollution indices (CF, PLI, RI) and the geo-accumulation index (I_geo). Multivariate analysis explores the relationships between metals and their potential sources. The results show significant differences in pollution levels (p < 0.05), with culture ponds having the highest pollution and ecological risk (RI = 73). As is the primary ecological risk factor (Er = 129). Zn and Cr are positively correlated with organic matter, while As and Pb show negative correlations with pH and salinity. Culture ponds increase heavy metal load and ecological risk, adversely impacting the mangrove ecosystem. These findings provide scientific support for land-use management and pollution control in mangrove wetlands.