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Ocean acidification poses serious threats to coastal ecosystem services, yet few empirical studies have investigated how local ecological processes may modulate global changes of pH from rising atmospheric CO2. We quantified patterns of pH variability as a function of atmospheric CO2 and local physical and biological processes at 83 sites over 25 years in the Salish Sea and two NE Pacific estuaries. Mean seawater pH decreased significantly at -0.009 +/- 0.0005 pH yr(-1) (0.22 pH over 25 years), with spatially variable rates ranging up to 10 times greater than atmospheric CO2-driven ocean acidification. Dissolved oxygen saturation (% DO) decreased by -0.24 +/- 0.036% yr(-1), with site-specific trends similar to pH. Mean pH shifted from < 7.6 in winter to > 8.0 in summer concomitant to the seasonal shift from heterotrophy (% DO < 100) to autotrophy (% DO > 100) and dramatic shifts in aragonite saturation state critical to shell-forming organisms (probability of undersaturation was > 80% in winter, but < 20% in summer). % DO overwhelmed the influence of atmospheric CO2, temperature and salinity on pH across scales. Collectively, these observations provide evidence that local ecosystem processes modulate ocean acidification, and support the adoption of an ecosystem perspective to ocean acidification and multiple stressors in productive aquatic habitats.