Wetlands play an essential role in the global carbon cycle, storing about 20% of terrestrial carbon while occupying only 5–8% of Earth’s land surface. They also account for roughly 30% of global methane emissions. However, these ecosystems are increasingly threatened by complex climate feedback controls and anthropogenic perturbations, which can disrupt their carbon balance. Hydrological disturbances—such as drought, flooding, and saltwater intrusion from sea-level rise—can significantly alter sediment biogeochemistry, impacting permanent carbon sequestration capacity and greenhouse gas fluxes. This research integrates fieldwork with laboratory bioreactors to examine how oxygen and sulfate influence the wetland microbiome. By pairing multi-omics approaches (metagenomics, transcriptomics, and proteomics) with measurements of microbial metabolites and greenhouse gas emissions, we aim to improve our understanding of wetland responses to environmental stressors—critical for predicting their role in future changes in weather patterns.