This report summarizes the activities of the NH Department of Environmental Services (NHDES) Shellfish Program for the period of January 2005 to December 2005, emphasizing those tasks for which NHDES received direct funding from the NH Estuaries Project. The NHDES Shellfish Program conducts a number of activities to minimize the health risks associated with consuming shellfish, and to continue to comply with National Shellfish Sanitation Program guidelines. Among basic program functions are a routine water quality monitoring program, red tide monitoring, and a pollution source identification and evaluation program. These sampling programs are supplemented by other activities aimed at improving the management of conditionally-approved harvesting areas. Augmented sampling in conditionally approved areas after rainfall events and/or sewage treatment plant upsets provides information to improve management decisions and, in some cases, increase harvesting opportunities. A study to compare results from two different bacterial analysis methods (the traditional fecal coliform Most Probable Number, or MPN, test, and a newer fecal coliform membrane filtration test using mTEC agar) was initiated in 2004 and continued through 2005. The results of the study will help DES determine how classification of growing areas might change if the less-expensive mTEC test is chosen to replace the traditional MPN method. Sanitary surveys were completed for Little Bay and the Bellamy River, and are near completion for Hampton/Seabrook Harbor, the Cocheco River, Salmon Falls River, and the Upper Piscataqua River. These are scheduled for completion in 2006.