Coral reefs were one of the first ecosystems to be recognized as vulnerable to ocean acidification. To date, most scientific investigations into the effects of ocean acidification on coral reefs have been related to the reefs’ unique ability to produce voluminous amounts of calcium carbonate. It has been estimated that the main reef-building organisms, corals and calcifying macroalgae, will calcify 10–50% less relative to pre-industrial rates by the middle of this century. This decreased calcification is likely to affect their ability to function within the ecosystem and will almost certainly affect the workings of the ecosystem itself. However, ocean acidification affects not only the organisms, but also the reefs they build. The decline in calcium carbonate production, coupled with an increase in calcium carbonate dissolution, will diminish reef building and the benefits that reefs provide, such as high structural complexity that supports biodiversity on reefs, and breakwater effects that protect shorelines and create quiet habitats for other ecosystems, such as mangroves and seagrass beds. The focus on calcification in reefs is warranted, but the responses of many other organisms, such as fish, noncalcifying algae, and seagrasses, to name a few, deserve a close look as well.