The purpose of this document is to review the existing state of knowledge for important physical, chemical, geological and biological components of the York River ecosystem within which the four individual reserve sites of Chesapeake Bay National Estuarine Research Reserve in Virginia (CBNERRVA) are located. It is developed from a combination of literature and field research studies that provide an overall picture of the Reserve in terms of its ecosystem, management, and research needs. This special issue is not designed to be a complete review of all the ecosystem components, but rather it is designed to provide, through a series of papers, an overview of the York system to students, researchers, resource managers and the general public, and to provide a system context for the individual reserve sites located within the York River estuary. It starts first with an introduction to the Reserve including its mission and objectives. Next the geological, physical and water quality setting of the individual reserve sites and the overall York River ecosystem are described. Scientific overviews of three important primary producer components and habitats within the region (phytoplankton, wetlands and submerged aquatic vegetation) are presented next. Secondary and higher trophic components (zooplankton, benthos, and fishes) are then reviewed, and finally the principal reptiles, amphibians, birds and mammals that are associated with the local estuarine waters are described. This Special Issue concludes with a description of the Reserve's ongoing research and monitoring programs, the Reserve goals and strategies, and an overview of research and monitoring needs for the future.