Marginal reef habitats are regarded as regions where coral reefs and coral communities reflect the effects of steady-state or long-term average environmental limitations. We used classifications based on this concept with predicted time-variant conditions of future climate to develop a scenario for the evolution of future marginality. Model results based on a conservative scenario of atmospheric CO2 increase were used to examine changes in sea surface temperature and aragonite saturation state over the Pacific Ocean basin until 2069. Results of the projections indicated that essentially all reef locations are likely to become marginal with respect to aragonite saturation state. Significant areas, including some with the highest biodiversity, are expected to experience high-temperature regimes that may be marginal, and additional areas will enter the borderline high temperature range that have experienced significant ENSO-related bleaching in the recent past. The positive effects of warming in areas that are presently marginal in terms of low temperature were limited. Conditions of the late 21st century do not lie outside the ranges in which present-day marginal reef systems occur. Adaptive and acclimative capabilities of organisms and communities will be critical in determining the future of coral reef ecosystems.