LAUSR

Abstract Extreme climatic events like floods and hurricanes have the potential to significantly alter coastal carbon cycling. However, due to the challenges associated with sampling these events, they can be difficult to incorporate into regional and global carbon budgets. To address this data gap, we bracket a major flooding event associated with the passing of Hurricane Joaquin (October 2015) with direct and high-resolution pCO2 measurements in the Neuse (NeuseRE) and New River Estuary (NewRE), North Carolina. Enhanced river discharge quickly flushed the relatively small NewRE, causing residence time to fall from 90 to 9 days, while the larger NeuseRE responded relatively slowly to flooding. This period of rapid flushing coincided with a significant increase in CO2 fluxes. The effect of cooler flood-waters, which reduce pCO2, was counteracted by allochthonous DIC inputs, which drove large increases in pCO2 relative to dissolved O2. The spatial distribution of carbonate buffering differed between estuaries, enhancing CO2 fluxes in the NewRE (178 mmol C m−2 d−1), while partially limiting air-water exchange in the NeuseRE (62 mmol C m−2 d−1). While windy storms may drive larger CO2 fluxes from estuaries, we show that flooding events can also contribute significantly to annual carbon budgets. CO2 emissions during this ~14-day flood period accounted for 31% (NeuseRE) to 44% (NewRE) of the total annual CO2 flux. Our findings show that sufficient spatial and temporal coverage during storms is necessary for estuarine CO2 fluxes to be reliably assessed over annual or longer time scales.