Disturbances are integral features of coral reefs, but since the 1970s they have degraded reefs throughout the world. While these events are well known, it is unclear how the perturbed communities will respond to further assaults. Here, we describe the effects of disturbances on reefs in St. John, US Virgin Islands, where coral cover has been < 4.5% for decades. In early 2010, seawater temperature exceeded values expected 95% of the time, but later in the year four storms brought 186 cm of rain that was 62% greater than the mean annual rainfall over 38 years. These storms increased terrigenous sedimentation and caused wave-induced re-suspension of benthic carbonate sediments. Rain-induced runoff was accentuated by overtopping of shoreline berms, and in the marine environment, a 10.5-fold elevation in the terrigenous accumulation and a 14.5-fold increase in re-suspended benthic carbonate sediments. The disturbances of 2010 were not clearly detectable by common indicators of reef condition, but were associated with 11-69% declines in coral recruitment, and increased densities of suspension-feeding polychaetes. Our results reveal the impacts of disturbances on coral reefs where low coral cover primes the community to display responses characterized by depressed coral recruitment and increased population sizes of polychaetes.