There are concerns about the future of coral reefs in the face of ocean acidification and warming, and while studies of these phenomena have advanced quickly, efforts have focused on pieces of the puzzle rather than integrating them to evaluate ecosystem level effects. The field is now poised to begin this task, but there are information gaps that first must be overcome before progress can be made. Many of these gaps focus on calcification at the levels of cells, organisms, populations, communities, and ecosystem, and their closure will be made difficult by the complexity of interdependent processes by which coral reefs respond to ocean acidification with effects scaling from cells to ecosystems, and from microns to kilometers. Existing ecological theories provide an important, and largely untapped resource for overcoming these difficulties, and they offer great potential for integrating the effects of ocean acidification across scales on coral reefs.