CBNERR has designed and implemented a System-wide Monitoring Program whose goal is to identify and track short-term variability and long-term changes in the integrity and biodiversity of representative estuarine ecosystems and coastal watersheds for the purpose of contributing to effective national, regional, and site specific coastal zone management. Currently this monitoring program includes water quality and meteorologic monitoring components.

Physical-chemical water quality is currently monitored semi-continuously (15 minute intervals) at the Virginia Reserve sites. Measured parameters include water temperature, salinity, dissolved oxygen, pH, turbidity, and water depth. This semi-continuous water quality monitoring program was initiated in 1995. Beginning in 2002, the Reserve began monitoring inorganic nutrients (ammonium, nitrate, nitrite, ortho-phosphate), total dissolved nitrogen and phosphorus, and chlorophyll at the Reserve sites. Meteorological conditions are also continuously monitored at Sweet Hall Marsh and Taskinas Creek (York River State Park). Stations record air temperature, relative humidity, rainfall, barometric pressure, wind speed and directions and photosynthetic active radiation (PAR). This program began in 1998.