Water quality parameters have been collected since 1995 with the establishment of the first water quality monitoring station at Potter Cove. Other three water quality stations (Nag Creek, T-Wharf Surface and T-Wharf Bottom, see map) were brought online in 2002. These stations represent a gradient in habitat types that range from salt marsh (Nag Creek station) to shallow cove (Potter Cove) to open Bay water (T-Wharf Surface and T-Wharf Bottom).

Water temperature, salinity, dissolved oxygen (% saturation, and mg L^-1), pH, turbidity, and chlorophyll fluorescence data are collected at each station every 15 minutes using YSI 6600 V2 and EXO2 data loggers.