Measurement of water column parameters were taken at 20 minute intervals in two locations within West Falmouth Harbor (West Falmouth, MA, USA), one in the well-flushed outer basin and one in the inner basin closer to the dominant groundwater N source. The goal of this dataset is to compare conditions at the two sites, as well as to derive rates of metabolism. Parameters measured include temperature, specific conducitity, salinity, dissolved oxygen, chlorophyll, and pH. YSI Datasondes were deployed during 4 periods ranging from 6 to 11 days in July and August, suspended vertically from a surface buoy. Over all deployments, instruments passed all QA checks, and average differences between the two instruments over all deployments were less than 0.06 degrees C (temperature), 0.3 (salinity), 0.05 (pH), 1.0 ug/L (chlorophyll), 1.5 (%DO Saturation). Data provided here are not corrected for drift, and chlorophyll data are uncorrected as reported by the instruments. Chlorophyll reported is uncorrected from the YSI calculation based on in-situ fluorescence and calibration with a single-point using deionized water. Lab fluorometric checks show that the YSI chlorophyll is over-reporting by approximately 20% at low concentrations, and high concentrations were not able to be validated.