Tidal freshwater wetlands are integral to downstream water quality because they capture, store, and transform nutrients. Unfortunately, anthropogenic stressors are negatively impacting these habitats. While wetland restoration is helping to reinstate their presence in the landscape, restored wetlands frequently differ physically, chemically, and biologically from their natural counterparts. This research examined plant, soil, and microbe relationships and how their interactions affect soil carbon (C) storage and cycling in natural and restored tidal freshwater wetlands of the Chesapeake Bay, MD, USA. This research yielded important findings regarding differences between natural and restored habitats. First, we discovered soil microbial community composition of an urban tidal freshwater wetland retained similar composition as their less disturbed, suburban counterpart, and wetland sites constructed using similar restoration methodology produced similar microbial community structure and soil function. Additional research revealed that a natural and a restored wetland store soil C quite differently: A majority of soil C in the natural site was associated with large macroaggregates (> 2000 μm) whereas most soil C in the restored site was associated with smaller macroaggregates (> 250 to < 2000 μm). The distributions of six chemical compound classes (i.e., carboxylics, cyclics, aliphatics, lignin derivatives, carbohydrates derivatives, N-containing compounds) were relatively similar across the five soil fractions from both sites, however. In the final study, anaerobic laboratory mesocosms were used to evaluate the effects of clay content (%) and leaf litter quality on soil C cycling processes over time. This study found restored soils, regardless of clay content, mineralized more C as carbon dioxide (CO2) and methane (CH4) compared to natural wetland soils. Natural soils respired approximately half the volume of gas as restored soils, suggesting the addition of high- or low-quality C substrates to low C systems elicit a greater response from the heterotrophic microbial community. The results of these three studies suggest site history and edaphic features of restored wetlands are important drivers of microbial communities and their function. We propose that practitioners and researchers work together to identify practices that will enhance soil functions, particularly C storage, in tidal freshwater wetlands of the Chesapeake Bay region.