The presence of hydrogen sulfide (H2S) gas in the muddy ecosystems is consequence of anthropogenic interference. To understand ecosystem health present study was intended to gauge H2S concentrations involved in annihilation of meiofauna and associated aquatic life from four hotspots including Manora channel, Korangi creeks, Sonmiani, and Bhambhore along the Pakistan coastal belt. Using a handheld gas detector device, it was observed that Bhambhore exhibited lower levels of H2S therefore embraces numerous benthic organisms whereas Manora channel (backwater) and Korangi creek area showed elevated level that does not allow macro-organisms to stay around. The diversity varied across locations, with Bhambhore collecting the most species of mudskippers and Manora creeks collecting the rarest. Overall result of this study reveals that H2S 5~274 ppm is alarming. The data of crabs, mudskippers, fishes, mantis shrimps, shells in relation to the environmental variables of temperature, salinity, conductivity dissolved oxygen and H2S were used to develop canonical correspondence analysis. The variability among first two components was 64.47 and 28.44%, eigenvalue (0.154, 0.068 and trace 0.239) respectively. Considering baseline findings of this study, greater efforts are required for ecosystem resilience for the sake of human health concerns.