The Peconic Estuary (Long Island, NY, USA) has experienced eelgrass retreat over the past two decades towards inlets or areas with increased ocean exchange, where water temperatures are cooler, similar to much of the US east coast. This project aims to identify shoreline segments where submarine groundwater discharge may provide cool water temperature refugia during the summer and to conduct eelgrass restoration in these areas. Here, we report on the identification and mapping of submarine groundwater discharge zones. We conducted airborne thermal infrared (TIR) flights over the Peconic Estuary in August and December 2023 to identify shoreline segments susceptible to submarine groundwater discharge. The presence of groundwater in the TIR imagery was validated through in-situ seawater mapping along the coast of temperature, salinity, radium, and radon-222, which are natural groundwater tracers. Results indicate significant TIR surface water anomalies throughout the Peconic Estuary, with reduced salinity and elevated radioisotope signatures. Two shoreline areas identified during summer were used for eelgrass test planting. Repeat TIR and radon measurements in winter confirmed the stability of submarine groundwater discharge as a potential thermal refugia zone. Intertidal and submarine groundwaters collected within these TIR zones further demonstrated enrichment of inorganic nutrients that varied with the seasonal migration of the freshwater-saltwater interface. This project serves as a model for eelgrass habitat restoration and implementation efforts in estuaries affected by groundwater inputs.