This research explored the influence of spatiotemporal variations in phreatic levels and salinity on the patterns and interactions of soil mesofauna communities in a tropical urban coastal wetland. It delineated significant variations in phreatic levels and salinity, with distinct regimes characterizing different habitats and hydroperiods. A total of 120 mesofauna morphotypes across 42 taxa were identified, revealing habitat differences and similarities, and the ecosystem biodiversity. Moderate correlations were established between phreatic levels, salinity, and mesofauna richness and abundance, with habitat type and phreatic level emerging as significant predictors in the regression model. Our findings indicate that shallow phreatic levels in conjunction with oligohaline salinity conditions foster a more favorable abiotic environment, thereby promoting increased biodiversity. The study underscores the dynamic and adaptive nature of mesofauna communities in response to changing environmental conditions, offering valuable insights for effective costal urban wetland management, particularly in the context of multiple stressors such as global and regional climate change, sea level rise, and human activities. The bio-sensor capacity of soil mesofauna emerges as a vital tool for monitoring and facilitating adaptive ecosystem management, thereby ensuring their long-term health and sustainability.