The presence of subaqueous soils in shallow aquatic habitats has been established in a number of diverse locations within the United States and further research is ongoing. The contribution of this work is the quantification of the biogeochemical function of subaqueous soils and the determination of how the structure and composition of distinct subaqueous soils influences their environmental role. We focus mainly on the biogeochemistry of N and P as these nutrients often limit primary productivity in both terrestrial and aquatic environments and are known to cause radical changes in ecosystem dynamics if not maintained by natural processes. The research takes place along the Chassahowitzka River, a coastal spring-fed river and estuarine system in NW Florida that acts as a hydrologic interface between the freshwater Floridian aquifer and the larger coastal environment and Gulf of Mexico. This geographic area is of particular concern as anthropogenic perturbations have increased nutrient loading at the springhead over time. Soils within the system are mapped, described, and evaluated using common soil metrics. Random sampling locations within map units are equipped with benthic flux chambers and monitored over time to determine nutrient flux rates within distinct map units. Finally, nutrient flux rates are evaluated with relation to soil composition allowing an inferred linkage to be made between soil composition and the biogeochemical role of a soil within the environment. Nutrient flux rates are extrapolated to the mapped extent of the soil map unit in order to provide an estimation of the overall significance of distinct soil map units in local biogeochemical cycling. Seasonal changes in nutrient flux rates will be reported in future work.