The National Estuarine Research Reserve System (NERRS), consisting of a network of 26 protected estuarine reserves in the conterminous US, Alaska, and Puerto Rico, generates comprehensive research and monitoring databases in support of coastal resource-management programs. Integrated water-quality, nutrient, and biological monitoring protocols conducted by the NERRS program have been valuable for identifying and tracking short-term variability and long-term changes in the integrity and biodiversity of estuarine systems nationwide. Four areas of biological monitoring in the NERRS program form the foundation for detailed research initiatives; these include (1) submerged aquatic vegetation (SAV) and emergent vegetation (marsh plants), (2) benthos (benthic invertebrates and benthic algae), (3) plankton (specifically larvae), and (4) nekton (fish, decapod crustaceans, and other swimming animals). Watershed and land-use/land-cover characterizations, benthic habitat mapping, and benthic community surveys comprise other high-priority initiatives of the NERRS program. The articles in this volume provide results of both system-wide investigations and site-specific case studies of the NERRS research and monitoring initiatives.