Estuarine wetlands are characterized by high biodiversity and active fluctuations in redox-sensitive metals (RSMs). In this study, sediment samples were collected from two sites, one with and one without vegetation, in the Yellow River Estuary Wetland (YREW). Active forms of Fe, Mn, and U were extracted using Tessier’s sequential extraction method, the bacterial community was analyzed through high-throughput sequencing, and the impact of the community on the RSMs was evaluated. The results indicated that the high nutrient content generated by vegetation withering had a positive effect on bacterial biodiversity, which led to high biomass and a wide variety of species in the sediments. Redox conditions and nutrient levels were the main factors influencing bacterial community structure. Under reducing conditions, genera such as Desulfococcus and Desulfosarcina were the main bacteria mediating the reduction of active Fe and Mn. Bacteria in genera such as Desulfatiglans and Desulfotomaculum were the main bacteria mediating the reduction of active U. These bacteria may result in obvious changes in the release of Fe, Mn, and U from salt marshes to nearshore regions. Our results can help to elucidate the interactions of bacteria and RSMs.