We often summarise monitoring data into general biodiversity indicators that help track and communicate changes in community structure, but which unfortunately also hide important details about what (or who) is changing. For example, the Community Temperature Index (CTI) has shown clear responses of reef fish communities to heatwaves, but whether this is actually ‘bad’ for biodiversity depends, in part, on how much of that change relates to species that were negatively impacted or disappeared. We developed a partitioning to tease apart the components of change in CTI to quantify the independent contributions of local extirpations, new species arriving into the community, and shifting abundances within persistent community members. Using the Reef Life Survey time series data collected at Rottnest Island since 2008, we showed how the changes observed during and following the extreme heatwave in 2011 unfolded not just through an influx of tropical fishes in 2011, but also extirpations of cool affinity species in 2011 and 2012 and reduced abundance of persistent cool affinity species in 2012. Thus, CTI increases at Rottnest Island clearly came with negative impacts for the local biodiversity, with the post-heatwave fish community lacking contributions of some of its former members.