Coral bleaching due to thermal and environmental stress threatens coral reefs and possibly people who rely on their resources. Here we explore patterns of coral bleaching and mortality in East Africa in 1998 and 2005 in a region where the equatorial current and the island effect of Madagascar interact to create different thermal and physicochemical environments. A variety of temperature statistics were calculated, and their relationships with the degree-heating months (DHM), a good predictor of coral bleaching, determined. Changes in coral cover were analyzed from 29 sites that span >1000 km of coastline from Kenya to the Comoros Islands. Temperature patterns are influenced by the island effect, and there are three main temperature environments based on the rise in temperature over 52 years, measures of temperature variation, and DHM. Offshore sites north of Madagascar that included the Comoros had low temperature rises, low DHM, high standard deviations (SD), and the lowest relative coral mortality. Coastal sites in Kenya had moderate temperature rises, the lowest temperature SD, high DHM, and the highest relative coral mortality. Coastal sites in the south had the highest temperature rises, moderate SD and DHM, and low relative coral mortality. Consequently, the rate of temperature rise was less important than background variation, as reflected by SD and kurtosis measures of sea surface water temperature (SST), in predicting coral survival across 1998. Coral bleaching responses to a warm-water anomaly in 2005 were also negatively related to temperature variation, but positively correlated with the speed of water flow. Separating these effects is difficult; however, both factors will be associated with current environments on the opposite sides of reefs and islands. Reefs in current shadows may represent refugia where corals acclimate and adapt to environmental variation, which better prepares them for rising temperature and anomalies, even though these sites are likely to experience the fastest rates of temperature rise. We suggest that these sites are a conservation priority and should be targeted for management and further ecological research in order to understand acclimation, adaptation, and resilience to climate change.