This study examined seafloor gas- and/or water-venting craters (pockmarks) to understand the drivers of the microorganisms inhabiting these environments. By combining lipid biomarkers extracted from seabed sediments with genetic analyses, the study found that the microbial community is shaped mainly by nitrogen availability, methane seepage, and porewater freshening. Pockmarks may therefore modulate coastal nutrient cycling and greenhouse gas dynamics, a finding relevant to ecosystem monitoring.