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Estuaries are generally considered a source of CO2 to the atmosphere, although with significant uncertainties in magnitude and controlling factors between and within estuaries. We studied four northwestern Gulf of Mexico estuaries that experience extreme hydrologic conditions between April 2014 and February 2017 to determine the role of dry/wet cycle on estuarine CO2 system. Annual air–water CO2 flux ranged from 2.7 to 35.9 mol·C·m−2·yr−1; CO2 flux declined by approximately an order of magnitude along with declining river discharge. Episodic flooding made CO2 flux differ between dry (−0.7 to 20.9 mmol·C·m−2·d−1) and wet (11.6–170.0 mmol·C·m–2·d–1) conditions. During wet condition, increases in dissolved inorganic carbon (DIC) and total alkalinity (TA) significantly elevated CO2 degassing. Furthermore, ventilation of river‐borne CO2 strengthened degassing when estuaries became overwhelmingly river‐dominated. During flood relaxation, all estuaries experienced heightened productivity, evidenced by DIC and TA consumption in the mid‐salinity range (10–30). When prolonged drought led to hypersalinity (>36.5), biogeochemical and evaporative effects enhanced DIC and TA consumption and CO2 degassing. Due to flooding and high wind speeds, these estuaries were a strong CO2 source during spring and summer. Then they transitioned to a weak CO2 source or sink during the fall. Low temperatures further depressed CO2 efflux during winter except when a pulse of freshwater input occurred. This study demonstrates that changes in the hydrologic condition of estuaries, such as dry/wet cycle and river discharge gradient, will greatly alter air–water CO2 flux and estuarine contribution to the global carbon budget.

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Two adjacent estuaries in the northwestern Gulf of Mexico (GOM) (Mission–Aransas or MAE and Guadalupe–San Antonio or GE), despite their close proximity and similar extents of freshening caused by Hurricane Harvey, exhibited different behaviors in their post-hurricane carbonate chemistry and CO2 fluxes. The oligotrophic MAE had little change in post-Harvey CO2 partial pressure (pCO2) and CO2 flux even though the center of Harvey passed right through, while GE showed a large post-Harvey increases in both pCO2 and CO2 flux, which were accompanied by a brief period of low dissolved oxygen (DO) conditions likely due to the large input of organic matter mobilized by the hurricane. The differences in the carbonate chemistry and CO2 fluxes were attributed to the differences in the watersheds from which these estuaries receive freshwater. The GE watershed is larger and covers urbanized areas, and, as a result, GE is considered relatively eutrophic. On the other hand, the MAE watershed is smaller, much less populous, and MAE is oligotrophic when river discharge is low. Despite that Harvey passed through MAE, the induced changes in carbonate chemistry and CO2 flux there were less conspicuous than those in GE. This study suggested that disturbances by strong storms to estuarine carbon cycle may not be uniform even on such a small spatial scale. Therefore, disparate responses to these disturbances need to be studied on a case-by-case basis.