Coastal wetland sediments are vital to the global carbon cycle as they represent large sinks of blue carbon – carbon from atmospheric and oceanic sources – which are threatened by ecosystem loss. The forms of sequestered carbon and the sequestration capability are affected by many bio- and geochemical factors that change unpredictably along coastal locales. In the present study, we investigated three unique coastal sites – a coastal mangrove and two sabkhas with contrasting geology and tidal influence in the Qatar peninsula – for their carbon capture ability to determine how biogeochemical indices affect their blue carbon sequestration potential. We applied a suite of biological and geochemical tools, collecting the sediment cores of approximately 40 cm depth; analysed sediment porewater; performed depth-profiling of the organic matter, sedimentary minerals, microbial community and analysis of sediment surface for pH, oxygen (O2); redox potential and hydrogen sulfide (H2S) by microsensors. High-resolution transmission electron microscopy with energy-dispersive X-ray spectroscopy (TEM-EDXS) and scanning transmission X-ray microscopy (STXM) revealed templating effects that promoted Mg-carbonate nucleation in coastal hypersaline environments. Microsensing reveals the intricacy of the oxic/anoxic transition at the sediment surface. Microbial DNA sequencing at various sediment depths shows the occurrence of microbial genera, whose functions explain the geochemical trends and carbon sequestration pathways observed at each site. Notably, we found that carbon sequestration in the mangrove and carbonate-sand sabkha was correlated with organic matter degradation and inorganic carbon content, while in the siliciclastic sabkha it was solely influenced by sediment density and depth.