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Anthropogenic climate change and associated increasing nutrient loading to coasts will worsen coastal eutrophication on a global scale. Basin Head is a coastal lagoon located in northeastern Prince Edward Island, Canada, with a federally protected ecosystem. Nitrate-nitrogen (NO3-N) is conveyed from agricultural fields in the watershed to the eutrophic lagoon via intertidal groundwater springs and groundwater-dominated tributaries. A field program focused on four main tributaries that discharge into the lagoon was conducted to measure year-round NO3-N loading. These measurements were used to calibrate a SWAT+ hydrologic model capable of simulating hydrologic and NO3-N loads to the lagoon. Several climate change scenarios incorporating different agricultural best management practices (BMPs) were simulated to better understand potential future NO3-N loading dynamics. Results indicate that all climate change scenarios produced increased annual NO3-N loading to the lagoon when comparing historical (1990–2020) to end of century time periods (2070–2100); however, only one climate scenario (MRI-ESM2-0 SSP5-8.5) resulted in a statistically significant (p-value