Mangrove forests are recognized for their capacity to store carbon. Their carbon dynamics can be significantly changed by anthropogenic disturbances, including nutrient loading from treated wastewater. This study investigates the effect of nutrient-enriched effluent from a domestic wastewater treatment on soil carbon storage in mangrove forests at The King’s Royally Initiated Laem Phak Bia Environmental Research and Development Project (LERD). The study area was conducted at two sites, including an experimental site and a reference site. Each site is divided into three zones from landward to seaward. The experimental site showed higher bulk density (BD), which may be caused by sediment compaction and nutrient-induced changes in soil structure. In contrast, both the percentage of organic carbon content (%OC) and soil carbon storage were lower compared to the reference site (p < 0.05). Soil carbon storage was estimated at 38.63 ± 5.28 and 45.07 ± 9.20 t C ha−1 in the experimental and reference sites, respectively. However, the experimental site showed greater values of diameter at breast height (DBH), stand height (H), aboveground biomass (AGB), and belowground biomass (BGB). These findings suggest that while nutrient loading may promote growth and biomass, it could enhance microbial decomposition processes. So, the soil’s capacity to store carbon was reduced in mangrove ecosystems.