This study assessed deep subsurface-to-surface transitional microbial communities in two serpentinizing ecosystems: a flaming gas/fluid seep in Yanartaş, Turkey and a bubbling fluid seep in Manleluag Spring National Park, the Philippines. These systems exhibited some similar geochemical and taxonomic attributes, but different physical properties that help demonstrate the effect surface conditions have on the subsurface. 16S rRNA gene sequencing, coupled with metagenomic and geochemical analysis, reveal dynamic microbial ecosystems supported partly by the products of active serpentinization. At Yanartaş, the fluid seeps may be ephemeral. Large travertine deposits are visible on the mountain slope as relicts of former fluid seeps. At Manleluag, the tropical climate causes monsoon and “dry” seasons, which influence dissolved inorganic and organic carbon input in the system. The 16S rRNA gene sequencing and metagenomic shotgun sequencing data suggest that, despite differences in regional climate and vegetation cover, Manleluag and Yanartaş exhibit taxonomic and functional similarities. Metabolisms involving methane, nitrogen, iron, and sulfur cycling, hydrogen oxidation, and respiration were detected in both 16S rRNA amplicon and metagenomic sequence datasets. Metagenomic analysis detected genes involved with osmotic and oxidative stress at both sites, and sporulation and dormancy genes at Manleluag. Several transposable elements were also reported at both Manleluag and Yanartaş. These mechanisms may allow subsurface microbial communities to adapt to surface conditions. In general, the surface and subsurface environment appear to be inherently connected at Yanartaş and Manleluag; the surface and subsurface both shape the microbial community in these ecosystems, and the microbial community alters the biogeochemistry.