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Groundwater discharge to rivers takes many forms, including preferential groundwater discharge points (PDPs) along riverbanks that are exposed at low flows, with multi-scale impacts on aquatic habitat and water quality. The physical controls on the spatial distribution of PDPs along riverbanks are not well-defined, rendering their prediction and representation in models challenging. To investigate the local riverbank sediment controls on PDP occurrence, we tested drone-based and handheld thermal infrared to efficiently map PDP locations along two mainstem rivers. Early in the study, we found drone imaging was better suited to locating tributary and stormwater inflows, which created relatively large water surface thermal anomalies in winter, compared to PDPs that often occurred at the sub-meter scale and beneath riparian tree canopy. Therefore, we primarily used handheld thermal infrared imaging from watercraft to map PDPs and larger seepage faces along 12-km of the fifth-order Housatonic River in Massachusetts, USA and 26-km of the Farmington River in Connecticut, USA. Overall, we mapped 31 riverbank PDPs along the Housatonic reach that meanders through lower permeability soils, and 104 PDPs along the Farmington reach that cuts through sandier sediments. Riverbank soil parameters extracted at PDP locations from the Soil Survey Geographic (SSURGO) database did not differ substantially from average bank soils along either reach, although the Farmington riverbank soils were on average 5× more permeable than Housatonic riverbank soils, likely contributing to the higher observed prevalence of PDPs. Dissolved oxygen measured in discharge water at these same PDPs varied widely, but showed no relation to measured sand, clay, or organic matter content in surficial soils indicating a lack of substantial near-surface aerobic reaction. The PDP locations were investigated for the presence of secondary bank structures, and commonly co-occurred with riparian tree root masses indicating the importance of localized physical controls on the spatial distribution of riverbank PDPs.