Wetland ecosystems may serve as either a source or a sink for atmospheric carbon andgreenhouse gases. This delicate carbon balance is influenced by the activity of belowgroundmicrobial communities that return carbon dioxide and methane to theatmosphere. Wetland restoration efforts in the San Francisco Bay-Delta region may helpto reverse land subsidence and possibly increase carbon storage in soils. However, theeffects of wetland restoration on microbial communities, which mediate soil metabolicactivity and carbon cycling, are poorly studied. In an effort to better understand theunderlying factors which shape the balance of carbon flux in wetland soils, we targetedthe microbial communities in a suite of restored and historic wetlands in the SanFrancisco Bay-Delta region. Using DNA and RNA sequencing, coupled with greenhousegas monitoring, we profiled the diversity and metabolic potential of the wetland soilmicrobial communities along biogeochemical and wetland age gradients. Our resultsshow relationships among geochemical gradients, availability of electron acceptors, andmicrobial community composition. Our study provides the first genomic glimpse intomicrobial populations in natural and restored wetlands of the San Francisco Bay-Deltaregion and provides a valuable benchmark for future studies.