Seawater pH, a measure of how acidic or basic water is, is a crucial water quality parameter influencing the growth and health of marine organisms, such as oysters, fishes and crabs. Decreasing pH, commonly referred to as acidification, is a severe environmental issue that has been exacerbated by human activities since the industrial revolution. In the open ocean, elevated atmospheric carbon dioxide is the key driver of acidification. However, in coastal environments the drivers are particularly complex due to changing human influences on land. In this study the primary drivers of acidification in the Chesapeake Bay over the past three decades are identified via the application of a three-dimensional ecosystem model. Increased atmospheric CO₂ concentrations and decreased terrestrial nutrient inputs are two primary drivers causing nearly equal reductions in pH in surface waters of the Bay. The pH reductions resulting from decreased nutrient loads indicate that the system is reverting back to more natural conditions when human-induced nutrient inputs to the Bay were lower. As nutrient reduction efforts to improve coastal water quality continue in the future, controlling the emissions of anthropogenic CO₂ globally becomes increasingly important for the shellfish industry and the ecosystem services it provides.