Abstract. Sustaining water quality is an important component of coastal resilience. Floodwaters deliver reactive nitrogen (including NOx) to sensitive aquatic systems and can diminish water quality. Coastal habitats in flooded areas can be effective at removing reactive nitrogen through denitrification (DNF). However, less is known about this biogeochemical process in urbanized environments. This study assessed the nitrogen removal capabilities of flooded habitats along an urban estuarine coastline in the upper Neuse River estuary, NC, USA, under two nitrate concentrations (16.8 and 52.3 µM NOx, respectively). We also determined how storm characteristics (e.g., precipitation and wind) affect water column NOx concentrations and consequently DNF by flooded habitats. Continuous flow sediment core incubation experiments quantified gas and nutrient fluxes across the sediment–water interface in marsh, swamp forest, undeveloped open space, stormwater pond, and shallow subtidal sediments. All habitats exhibited net DNF. Additionally, all habitats increased DNF rates under elevated nitrate conditions compared to low nitrate. Structured habitats with high-sediment organic matter had higher nitrogen removal capacity than unstructured, low-sediment organic matter habitats. High-precipitation–high-wind-storm events produced NOx concentrations significantly lower than other types of storms (e.g., low-precipitation–high-wind, high-wind–low-precipitation, low-wind–low-precipitation), which likely results in relatively low DNF rates by flooded habitats and low removal percentages of total dissolved nitrogen loads. These results demonstrate the importance of natural systems to water quality in urbanized coastal areas subject to flooding.