Estuaries are one of the most biogeochemically active ecosystems on Earth where intense carbon (C) fixation and respiration drive large air-water CO2 fluxes. The complexity of these interactions and a paucity of available data lead to substantial uncertainty when integrating estuarine CO2 fluxes into regional and global C budgets. This dissertation focuses on characterizing the processes that regulate gas exchange and quantitatively improving estuarine CO2 flux estimates. 57 high-resolution surveys were conducted between 2009 and 2011 to quantify the spatial and temporal variability of air-water CO2 fluxes in a large microtidal estuary system, the Neuse River Estuary- Pamlico Sound, NC. CO2 fluxes were highly dependent on the environmental conditions and showed large variability in time and space. Contrary to the traditional view of estuaries as larges sources of CO2 to the atmosphere, the study systems varied between a small annual CO2 source and sink, implying that global estimates of estuarine CO2 efflux need to be revised. In August 2011, Hurricane Irene passed directly over the study area. The storm mobilized C that would have otherwise been stored in terrestrial and coastal ecosystems and much of this C was released to the atmosphere from estuarine waters. Irene-induced CO2 efflux from Albermarle-Pamlico Sound (APS) system was estimated to offset 2.5 years of C sequestration in the APS watershed. Tropical cyclones like Irene are projected to become more intense as global temperatures rise, which will likely impact the role of coastal systems in C sequestration and long-term storage. Bubbles generated by breaking waves can drive large air-water gas exchanges in open, oceanic water, but the role of bubble-mediated gas exchange in estuaries is unknown. Archival backscatter data from 41 acoustic Doppler current profiler stations was analyzed to assess subsurface bubble distributions in 9 estuaries. Statistical analysis showed that bubble entrainment in estuaries began at relatively low wind speeds but varied due to site-specific differences in geophysical characteristics. Data observed during several storms suggests that episodic events can have a major impact on CO2 fluxes in large, shallow estuaries. Better representation of estuarine gas transfer velocities will greatly reduce uncertainties in estuarine CO2 fluxes.