Low stream flows in the Fenton River, part of a hydrogeological setting characterized by glacial stratified drift, forces the University of Connecticut to frequently reduce groundwater withdrawals during the months of June–October. The objective of this study was to investigate stream/aquifer interactions in such a hydrogeologic system in order to increase water withdrawals while minimizing adverse impacts to in-stream flow. A groundwater flow model was developed using MODFLOW to investigate the influence of well location and pumping timing on in-stream flow in the vicinity of the water supply wells. The numerical model comprised detailed geophysical data and decadal hydrologic data (2000–2009) to assess well placement, rest periods and cyclical pumping. The relocation of a water supply well up to 228 m from the river had a positive but minimal improvement to stream flows (<2.83 L/s). When the well field was shut off for more than 45 days, stream flows returned to the no pumping condition with only slight impact at 30 days, whereas a 30 day rest period gave 4 weeks of dampened pumping influence on stream flows. A management scenario of 1 week cyclical pumping between two water supply wells following a 45 day rest period can allow for current restriction thresholds to be reduced by 28.3 L/s with minimal impact to stream flows (7.36 L/s) and would allow additional water to be pumped for all years in which there was a demand for water.