The southern Great Barrier Reef (GBR), a region that rarely experiences cyclones, was impacted by tropical cyclone (TC) Hamish in March 2009. We documented on-reef physical and habitat conditions before, during and after the cyclone at One Tree Reef (OTR) using data from environmental sensor instrumentation and benthic surveys. Over 5 years of monitoring, ocean mooring data revealed that OTR experienced large swells (4–8 m) of short duration (10–20 min) not associated with a cyclone in the area. These swells may have contributed to the physical disturbance of benthic biota and decline in coral cover recorded prior to and after TC Hamish. During the cyclone, OTR sustained southeasterly gale force winds (>61.2 km h−1) for 18.5 h and swells >6 m in height for 4 h. Benthic surveys of exposed sites documented a 20% drop in live coral cover, 30% increase in filamentous algae cover and the presence of dislodged corals and rubble after the storm. Leeward sites were largely unaffected by the cyclone. Benthic cover did not change in the lagoon sites. Significant rubble movement and infill of the lagoon occurred. Two years after the cyclone, algal cover remained high and laminar corals had not recovered. Total coral cover at impacted sites had continued to decline. Environmental conditions and habitat surveys supported Puotinen's (Int J Geogr Inf Sci 21:97–120, 2007) model for cyclone conditions that cause reef destruction. While TC Hamish had a major impact on the reef, change in benthic cover over several years was due to multiple stressors. This on-reef scale integration of physical and biological data provided a rare opportunity to assess impacts of a major storm and other disturbances, showing the importance of considering multiple stressors (short-lived and sustained) in assessing change to reef habitats.