In the context of global environmental change, barrier islands are a sentinel world region increasingly vulnerable to seawater flooding from storms and rising sea levels. Coastal floods erode dunes and salinize fresh groundwater resources that support island ecosystems and populations; however, the connection between storm-driven flooding, erosion, and saltwater intrusion (SWI) is poorly understood. This study monitored how the morphology and fresh groundwater resources of a barrier island (Hog Island, Pituamkek in Mi’kmaq) in PEI responded to flooding from post-tropical storm Fiona (24 September 2022), the costliest hurricane to make landfall in Canadian history. Pre-disturbance, post-disturbance, and early-recovery surveys monitored island morphology with drone-based LiDAR and groundwater salinity and level dynamics with frequency-domain electromagnetic geophysics and monitoring wells. High storm surge and waves undercut the foredune, causing widespread scarping, and the infiltration of floodwaters completely saturated beach sediments with seawater. On average, 10 m of lateral erosion occurred, and all fresh groundwater under the eroded dune was salinized. Nine months after the storm, morphologic recovery was limited, and only 1% of the island volume that eroded (12%) was returned. High dune scarps remained, and without a stable foredune, flooding from winter storms limited beach aquifer flushing and recovery. Results reveal an often-overlooked connection between episodic flooding, erosion, and groundwater salinization that exacerbates the loss of freshwater from coastal floods. This finding is important to inform coastal management in an age of rising seas and more frequent and intense coastal storms, particularly for this Mi’kmaq heritage site and national park reserve.