Shallow coastal ecosystems are already experiencing thermal stress and will likely continue to warm under ongoing atmospheric and oceanic climate change. However, the magnitudes of temperature changes in shallow coastal waters in response to climate change are subject to large uncertainties because coastal water temperature patterns in these settings are influenced by interacting atmospheric heat fluxes, advective freshwater inputs, and thermal oceanic exchange. There is therefore a need to examine how concurrent changes in watershed hydrology, sea level, and atmospheric conditions may thermally influence coastal waters. Accordingly, we applied a calibrated hydrodynamic model (MIKE 21FM) coupled with a thermal module to investigate changes in the spatiotemporal temperature patterns of a federally protected lagoon in eastern Canada. Atmospheric projections from two downscaled global climate models under two Shared Socioeconomic Pathways, together with scenarios of altered freshwater inflow temperature and discharge and varying rates of sea-level rise, were implemented as model boundary conditions and associated model run scenarios. Results were analyzed for two 20-year intervals representing historical (2000–2020) and end-of-century (2080–2100) conditions. Results indicate that the lagoon may experience significant warming (up to 3.9°C) in summer by the end of the century, with changing atmospheric forcing emerging as the dominant driver of lagoon-wide warming. Conversely, moderate to high rates of sea-level rise can partially offset temperature increases by enhancing cooling from lagoon–ocean exchange. Results also reveal pronounced spatial thermal heterogeneity, with the cooling influence of freshwater inflows from groundwater springs and tributaries remaining highly localized under future climate conditions.