Most subaqueous soil (SAS) research to date has occurred in coastal and marine environments and has yet to explore freshwater systems in order to develop appropriate taxonomic classifications and Soil Survey interpretations. Freshwater SAS research has great potential to provide further understanding of carbon sequestration and enhanced water quality management, especially in reservoir systems. Pennsylvania has an abundance of freshwater systems, however many are impaired by mercury. Additionally, some of Pennsylvania’s reservoirs, such as this study’s research site at Black Moshannon Lake, are located in environments tending to accumulate mercury, which is tightly associated with organic carbon in transport and storage across a landscape. We present preliminary results of research that examines pedogenic changes in subaerial soils upon flooding, and their subsequent evolution into subaqueous soils. Our research characterizes and maps the extent of SASs using appropriate taxonomy and landscape features, and determines the distribution of mercury in soils across the landscape hydrosequence.