We used spatial data from previously mapped preferential groundwater discharges throughout the Farmington River watershed in Connecticut and Massachusetts (https://doi.org/10.5066/P915E8JY) to guide water sample collection at known locations of groundwater discharging to surface water. In 2017 and 2019 - 2021, samples were collected during general river baseflow conditions (July – November, <30.9 cms mean daily discharge (USGS gage 01189995, statistics 2010-2022) when the riverbank discharge points were exposed. We collected a suite of dissolved constituents and stable isotopes of water directly in the shallow saturated sediments of active points of discharge, and coincident stream chemical samples were also collected adjacent to locations of groundwater discharge. Data collected includes nutrients (NO3, NH4, Cl, SO4, PO4, dissolved organic carbon (DOC), and total nitrogen (TN)), greenhouse gases (CO2, CH4, and N2O), dissolved gases (N2, dissolved oxygen (DO)), conductivity, sediment characteristics, temperature, and spatial information. This dataset includes 2 main files: 1) Farmington_Chemistry_2017_2021.csv contains attribute information for each biogeochemical constituent collected at preferential groundwater discharges along the Farmington River network. 2)Farmington_Temporal_Cl_Rn_Iso_2020.csv contain attribute information for source characteristic data (Chloride, Radon, Isotope) collected at locations of repeat sampling at 5 groundwater seep faces along the Farmington River (Alsop and Rainbow Island).