AbstractIn estuaries, local processes such as changing material loads from the watershed and complex circulation create dynamic environments with respect to ecosystem metabolism and carbonate chemistry that can strongly modulate impacts of global atmospheric CO₂ increases on estuarine pH. Long‐term (> 20 yr) surface water pH records from the USA's two largest estuaries, Chesapeake Bay (CB) and Neuse River Estuary‐Pamlico Sound (NRE‐PS) were examined to understand the relative importance of atmospheric forcing vs. local processes in controlling pH. At the estuaries’ heads, pH increases in CB and decreases in NRE‐PS were driven primarily by changing ratios of river alkalinity to dissolved inorganic carbon concentrations. In upper reaches of CB and middle reaches of the NRE‐PS, pH increases were associated with increases in phytoplankton biomass. There was no significant pH change in the lower NRE‐PS and only the polyhaline CB showed a pH decline consistent with ocean acidification. In both estuaries, interannual pH variability showed robust, positive correlations with chlorophyll a (Chl a) during the spring in mid to lower estuarine regions indicative of strong control by net phytoplankton production. During summer and fall, Chl a and pH negatively correlated in lower regions of both estuaries, given a shift toward heterotrophy driven by changes in phytoplankton community structure and increases in the load ratio of dissolved inorganic nitrogen to organic carbon. Tropical cyclones episodically depressed pH due to vertical mixing of CO₂ rich bottom waters and post‐storm terrestrial organic matter loading. Local processes we highlight represent a significant challenge for predicting future estuarine pH.