A comprehensive survey of the current biota and their environment is desireable prior to deployment of shell or broodstock oysters to establish a system baseline for oyster populations. Such a baseline is particularly important in estuaries without public oyster grounds and regularly scheduled stock assessment surveys. Comprehensive system surveys include two main elements: habitat mapping and oyster population assessment.

A detailed and data rich map of habitats, including information that will later relate to abundance estimates, size structure and patterns of settlement, disease and genetics is required. Data will subsequently be used to design detailed field sampling and will serve as the base for GIS data integration. Habitats will be mapped and specific information, collected in the field, will be attached to positions utilizing precise post-processed GPS data and a data logger. Information will then be incorporated into an ArcGIS database. Initial mapping data will be used to focus subsequent biological sampling. Biological data will be collected from each habitat type in each basin section.Replicated quadrat samples will be collected to determine oyster density and size by each habitat type.

Oyster estimates will be coupled with earlier mapping to provide a basic demographic model for the entire system. This information will provide a detailed description of the oyster population prior to deployment and can be compared to data collected utilizing similar protocols in the future to elucidate the impacts of the overall restoration project.