Coastal water temperatures may rise in the coming decades, as oceans warm and as inflowing river water temperatures are influenced by changing atmospheric conditions. Although a large body of research has focused on the thermal regimes of rivers and lakes, little work has been conducted on the thermal regimes of transitional, coastal water bodies. Water temperature is an important water quality parameter, and its sensitivity to meteorological and hydrological forcing plays a significant role in controlling the health of aquatic ecoystems. However, few studies have quantitatively considered the thermal sensitivity of coastal waters to atmospheric and marine climate change (sea-level rise and ocean warming). We focus this study in the Basin Head lagoon, a Marine Protected Area in eastern PEI that supports an endemic population of giant Irish moss that is threatened by rising lagoon temperatures, eutrophication, and invasive species. We apply a coastal hydrodynamic model coupled with a temperature module (DHI, 2022) to simulate the influence of changing atmospheric, riverine (temperature and flow rates), and marine boundary conditions. Field data (tidal levels, salinity, and temperature) are used to calibrate and assess the numerical model performance. Results highlight potential impacts of climate change (on lagoon water temperatures and associated ecological dynamics, with both marine and atmospheric changes exerting influence. A large uncertainty in the future lagoon warming due to climate change relates to the bathymetric response to sea-level rise.