Alkalinity, which is the capacity of a water body to neutralize acid, is a useful quantity when studying the cycling of carbon in water bodies, including estuaries. Here we analyze alkalinity measurements in tidal tributaries of the Chesapeake Bay. Average alkalinity levels in the freshest parts of the estuaries varied by sixfold among seven tidal tributaries. Alkalinity was also found to increase over several decades at several locations, partially due to alkalinity increases in the rivers draining to Chesapeake Bay and also probably due to a reduction in the processes that remove alkalinity from estuarine waters. Evidence also supports the role of an invasive species, the Asiatic Clam, in the alkalinity removal in the Potomac River Estuary. More generally, we found evidence that tidal tributaries fed by high-alkalinity rivers consumed alkalinity while tidal tributaries that are fed by low-alkalinity rivers produce alkalinity. For a single estuarine system, the Chesapeake Bay has a wide range of alkalinity levels and a wide variety of processes that influence its alkalinity. Therefore, the Chesapeake Bay can serve as a laboratory for studying the alkalinity of many of the world’s estuaries.