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<p>In inland settings, groundwater discharge thermally modulates receiving surface water bodies and provides localized thermal refuges; however, the thermal influence of intertidal springs on coastal waters and their thermal sensitivity to climate change are not well studied. We addressed this knowledge gap with a field- and model-based study of a threatened coastal lagoon ecosystem in southeastern Canada. We paired analyses of drone-based thermal imagery with in situ thermal and hydrologic monitoring to estimate discharge to the lagoon from intertidal springs and groundwater-dominated streams in summer 2020. Results, which were generally supported by independent radon-based groundwater discharge estimates, revealed that combined summertime spring inflows (0.047 m<span class="inline-formula">³</span> s<span class="inline-formula">⁻¹</span>) were comparable to combined stream inflows (0.050 m<span class="inline-formula">³</span> s<span class="inline-formula">⁻¹</span>). Net advection values for the streams and springs were also comparable to each other but were 2 orders of magnitude less than the downwelling shortwave radiation across the lagoon. Although lagoon-scale thermal effects of groundwater inflows were small compared to atmospheric forcing, spring discharge dominated heat transfer at a local scale, creating pronounced cold-water plumes along the shoreline.</p> <p>A numerical model was used to interpret measured groundwater temperature data and investigate seasonal and multi-decadal groundwater temperature patterns. Modelled seasonal temperatures were used to relate measured spring temperatures to their respective aquifer source depths, while multi-decadal simulations forced by historic and projected climate data were used to assess long-term groundwater warming. Based on the 2020–2100 climate scenarios (for which 5-year-averaged air temperature increased up to 4.32<span class="inline-formula">^∘</span>), modelled 5-year-averaged subsurface temperatures increased 0.08–2.23<span class="inline-formula">^∘</span> in shallow groundwater (4.2 m depth) and 0.32–1.42<span class="inline-formula">^∘</span> in the deeper portion of the aquifer (13.9 m), indicating the depth dependency of warming. This study presents the first analysis of the thermal sensitivity of groundwater-dependent coastal ecosystems to climate change and indicates that coastal ecosystem management should consider potential impacts of groundwater warming.</p>