The Massachusetts Division of Fisheries and Wildlife has been studying brook trout populations in Cape Cod groundwater-fed river systems for decades. Recently, a notable reduction in trout population in the Santuit River sparked the concern of several groups, including the Wampanoag Tribe. Brook trout population dynamics may be tied to water quality and temperature changes, which are both impacted by spatially preferential groundwater discharge to the river. The streambed interface temperature and near-surface geophysical data compiled in this data release were collected in summer 2018 as part of a larger effort to characterize the spatial distribution of groundwater discharge zones, and exchanges with surface water, along Cape Cod stream systems. Fiber-optic distributed temperature sensing (FO-DTS) cables were deployed along the sediment/water interface to map high spatial resolution temperature variations along the streambed that are used to locate discharges. Geophysical data include towed ground penetrating radar (GPR) data to image near surface streambed structure, and hand-carried electromagnetic imaging (EMI) data to indicate changes in streambed water quality and/or near surface sediments. Therefore, this combined dataset represents point-in-time mapping of preferential groundwater discharge points (FO-DTS), and the bed structure that controls where these points are located (GPR, EMI).