We present findings from recent carbon modeling studies and 5 years of carbon sampling in the Georgia and Juan de Fuca Straits. Near-surface pH and aragonite saturation state (ΩA) are highly variable (temporally and with depth) in stratified areas like the Strait of Georgia, and vary less in well-mixed areas like Juan de Fuca Strait and the San Juan Islands. Strong seasonal productivity increases Strait of Georgia surface pH and ΩA during summer, but these waters are naturally corrosive (aragonite-undersaturated) during winter and below 20 m depth. Several potentially acidification-sensitive species of plankton and shellfish reside at least partially within these corrosive zones. Strong Fraser River freshets can offset surface pH and ΩA increases because of low-salinity carbon dynamics, river shading of phytoplankton, and calcium dilution. Estuarine-driven inflows from the Pacific Ocean characterize the deep Juan de Fuca Strait and are carbon-rich during the upwelling season. However, these inflows effectively increase pH and ΩA in the Strait of Georgia because of local carbon retention. These findings may provide insights into several areas of marine management including preservation area planning, aquaculture best practices, and seasonal fisheries forecasting