Hurricanes that damage lives and property can also impact pollutant sources and trigger poor water quality. Yet, these water quality impacts that affect both human and natural communities are difficult to quantify. We developed an operational remote sensing-based hurricane flood extent mapping method, examined potential water quality implications of two "500-year" hurricanes in 2016 and 2018, and identified options to increase social-ecological resilience in North Carolina. Flooding detected with synthetic aperture radar (>91% accuracy) extended beyond state-mapped hazard zones. Furthermore, the legal floodplain underestimated impacts for communities with higher proportions of older adults, disabilities, unemployment, and mobile homes, as well as for headwater streams with restricted elevation gradients. Pollution sources were repeatedly affected, including ∼55% of wastewater treatment plant capacity and swine operations that generate ∼500 M tons/y manure. We identified ∼4.8 million km2 for possible forest and wetland conservation and ∼1.7 million km2 for restoration or altered management opportunities. The results suggest that current hazard mapping is inadequate for resilience planning; increased storm frequency and intensity necessitate modification of design standards, land-use policies, and infrastructure operation. Implementation of interventions can be guided by a greater understanding of social-ecological vulnerabilities within hazard and exposure areas.