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Coastal wetlands, vital for ecological diversity, have been significantly altered by anthropogenic activities, particularly in the Caribbean. These changes have created a complex mosaic of habitats and physicochemical conditions, further stressed by climate variability and sea-level rise. This study, conducted in Las Cucharillas Natural Reserve, a tropical urban coastal wetland in Puerto Rico, aimed to determine the effects of spatiotemporal variations in phreatic levels and salinity on soil mesofauna assemblages, crucial bio-indicators of environmental change. In 2020 and 2021, soil samples were collected from five diverse habitat types during different hydroperiods. Each sample was taken under four randomly selected plant types and processed using lighted Tullgren–Berlese extractors. Phreatic level and salinity were also measured. A total of 43 families were quantified, underscoring distinct habitat differences, similarities, and overall ecosystem diversity. Moderate correlations between phreatic levels, salinity, and mesofauna richness and abundance were determined. Peak richness and abundance were quantified at shallow (−0.03 to −0.07 m) and slightly moderate (−0.12 to −0.17 m) phreatic levels where oligohaline salinity (>0.5 to 5.0 ppt) prevails. The study highlights the adaptability of mesofauna to environmental shifts and their potential as biosensors for effective coastal wetland management amid climatic and anthropogenic pressures.