Benthic organisms and their communities are key components of estuarine systems. We provide an overview of the biology and key ecological features of benthic communities of York River Estuary (YRE), which is the site of the Chesapeake Bay National Estuarine Research Reserve in Virginia (CBNERRVA). Major subtidal benthic habitats in YRE include soft mud and sand bottoms, with only limited distribution of submerged aquatic vegetation and oyster shell. Major taxonomic groups of macrofauna dominating muds and sands of YRE include annelids, molluscs and crustaceans; similar to those found in other temperate estuaries of the US Mid-Atlantic. Meiofaunal assemblages of YRE soft bottoms are dominated by nematodes and copepods. Species distribution patterns in YRE are strongly correlated with salinity and bottom type, while other factors such as eutrophication and hypoxia may be growing in importance. Much of the YRE benthos fails to meet the restoration goals set by the Chesapeake Bay Program. The poor condition of the benthos is expressed as low biomass and abundance and may be associated with degraded water quality, hypoxia and sediment disturbance processes. No comprehensive inventory of the benthic biota of the CBNERRS sites is available, which will make it difficult to assess future changes due to human impacts such as climate change or the introduction of exotic species. Given this paucity of data, a systemic cataloging of the benthic resources of the reserve sites and any potential invasive species is a much needed avenue of future research for CBNERRVA.