Coastal ecosystems persist in a highly dynamic environment, especially with respect to pH. This high spatiotemporal variability of pH is driven by complex physical and biological processes that complicate climate change predictions. Using coral reefs and rocky intertidal ecosystems as examples, I discuss several case studies that highlight how pH, in combination with other anthropogenic stressors, affect ecosystem functioning. Specifically, I focus on how ecosystem function is affected by direct effects of climate change, natural pH variability across multiple spatial scales, and biological feedbacks. Understanding the natural variability of coastal ecosystems and how organisms both drive and respond to changes in pH is necessary to project how ecosystem functioning will change in the future.