Although the extent of subaqueous soils in coastal areas is obvious, and their importance in regard to the structure and function of the estuarine ecosystem is unquestionable, little is known of the physical, chemical, and morphologic properties of subaqueous soils and how they developed in these ecosystems. The information that is available has been gathered from a limited number of research projects (Demas et al., 1996; Demas, 1998; Demas and Rabenhorst, 1998; Bradley, 2001; Bradley and Stolt, 2002; Bradley and Stolt, 2003; Bradley and Stolt, 2005). These studies have spawned a wide array of interest in subaqueous soils such that subaqueous soil projects have been initiated in Connecticut, New York, Maine, Delaware, Maryland, Florida, Massachusetts, Rhode Island, and Texas. One of the big hurdles of these studies is that only minimal information on methodologies that are appropriate for conducting a subaqueous soil survey is available. Discussions on topics such as collecting bathymetric data, using a vibracore, collecting soil samples under water, and the handling of subaqueous soil samples for subsequent laboratory analysis are essentially absent from the soil literature. Thus, there is a need for a standard reference source on the methodologies used to conduct a subaqueous soil survey. In this paper, methods for sampling and analysis of subaqueous soils are discussed and illustrated.