Increased nutrient loading to estuaries has led to eutrophication, degraded water quality, and ecological transformations. Quantifying nutrient loads in systems with significant groundwater input can be difficult due to the challenge of measuring groundwater fluxes. We quantified tidal and freshwater fluxes over an 8-week period at the entrance of West Falmouth Harbor, Massachusetts, a eutrophic, groundwater-fed estuary. Fluxes were estimated from velocity and salinity measurements and a total exchange flow (TEF) methodology. Intermittent cross-sectional measurements of velocity and salinity were used to convert point measurements to cross-sectionally averaged values over the entire deployment (index relationships). The estimated mean freshwater flux (0.19 m3/s) for the 8-week period was mainly due to groundwater input (0.21 m3/s) with contributions from precipitation to the estuary surface (0.026 m3/s) and removal by evaporation (0.048 m3/s). Spring–neap variations in freshwater export that appeared in shorter-term averages were mostly artifacts of the index relationships. Hydrodynamic modeling with steady groundwater input demonstrated that while the TEF methodology resolves the freshwater flux signal, calibration of the index–salinity relationships during spring tide conditions only was responsible for most of the spring–neap signal. The mean freshwater flux over the entire period estimated from the combination of the index-velocity, index–salinity, and TEF calculations were consistent with the model, suggesting that this methodology is a reliable way of estimating freshwater fluxes in the estuary over timescales greater than the spring–neap cycle. Combining this type of field campaign with hydrodynamic modeling provides guidance for estimating both magnitude of groundwater input and estuarine storage of freshwater and sets the stage for robust estimation of the nutrient load in groundwater.