High-latitude coral reef communities have been postulated as the first areas to undergo reorganisation under climate change. Tropicalisation has been identified in some high-latitude communities and is predicted in others, but it is unclear how the resident benthic taxa are affected. We conducted a long-term (2007–2016) assessment of changes to benthic community cover in relation to thermal stress duration on the Southeast Florida Reef Tract (SEFRT). Thermal stress events, both hot and cold, had acute (thermal stress duration affected benthic cover that year) and chronic (thermal stress duration affected benthic cover the following year) impacts on benthic cover. Chronic heat stress was associated with declines in cover of the reef-building coral families Acroporidae, Montastraeidae, Meandrinidae, Mussidae and Siderastreidae, which coupled with the absence of cold stress and rising annual temperatures boosted macroalgae cover. Cover of smaller, weedy coral families, Poritidae, Agariciidae and Astrocoeniidae, was either unaffected or positively related to heat stress duration and rising mean temperature. Thermal stress was related to spatiotemporal variations in benthic cover on the SEFRT, likely enhanced by local stressors, such as elevated nutrients and sedimentation. Coral and octocoral cover declined within four of six sub-regions, sponge cover increased in half of the sub-regions, and macroalgae cover increased in four sub-regions during the study. Under current conditions, increased macroalgae and weedy coral cover are anticipated to inhibit reef recovery.