The National Shellfish Indicator Study (NSIS) is a project that will develop new technology for microbiological methods that can be used to effectively evaluate the actual risk to public health from human sewage pollution of shellfish growing waters. This is a collaborative effort of university, industry and shellfish regulatory members from the shellfish producing and receiving areas in the United States. This report details Phase II of Estuarine Site Selection in the development of the Background Studies for the work in progress with the Louisiana State Universities Marine Consortium and the National Oceanic and Atmospheric Administration. The selected sites are where the extensive collaborative microbiological field studies will be conducted to evaluate levels of standard and new indicators.