Soils and sediments make up a substantial portion of the resource base that supports human societies and other life on Earth, yet in the subaqueous environment our understanding of these materials pales in comparison to our understanding and management of upland soils. We must develop an understanding of how subaqueous soils/sediments are distributed, how they form and change over time, and how they will be impacted by rising sea-levels as a result of climate change if we are to wisely manage these resources. The goal of this study is to improve this understanding in Chesapeake Bay subestuaries. The Rhode River subestuary was first surveyed to identify rates of bathymetric change in these settings and to characterize the common material types found in these settings. Bathymetric change was evaluated using hydrographic surveys dating back to 1846, and though the river bottom does change slowly, it has been more or less stable during the years evaluated. Several types of morphologically distinct materials make up the soil profiles in Rhode River. Materials highest in organic matter are easy to identify in the field, and commonly become ultra-acidic if disturbed. Also present were submerged upland soils, colored and structured like soils in the surrounding landscape. To better understand the impacts of submergence on these materials, a sampling campaign was conducted on shallow marine sediments, reclaimed land, and restored aquatic environments under both seawater and freshwater. This demonstrated that shallow marine sediments develop upland soil features and biogeochemical characteristics within 150 years of drainage, and that these characteristics do indeed persist in the subsoil two years after submergence. Topsoil changes more radically, releasing anomalous amounts of Fe while accumulating anomalous amounts of reduced S minerals, a process exacerbated by seawater flooding. Using these results, a soil-landscape conceptual model was developed and used to predict subaqueous soil distribution in the West River subestuary. These predictions were evaluated with a sampling campaign, and found to be significant. This model can now be used in other subestuaries to quickly and efficiently survey subaqueous soils, supporting the development of future land-use interpretations in these environments.