Southwest Australia (SWA) is among the world's most prominent ocean warming hotspots, with temperatures rising faster than the global average and driving shifts in fish community composition. We use a long-term regional dataset to assess fish assemblage stability across multiple areas and depth in SWA. Shallow reefs (5-20m) were surveyed on four occasions between 2006 and 2023 using diver-operated stereo video and remotely operated vehicles (ROVs) across 2000km of coastline. Following the 2010/2011 marine heatwave, nearly the entire study area underwent substantial reorganisation, with subtropical and tropical species increasing in abundance and seeming to persist in cooler ecosystems with further evidence of ongoing compositional shifts evident in both warm and cool regions. Shifts in keystone habitat species Ecklonia radiata and increasing sea surface temperature were key environmental drivers, linked to these shifts. Although the magnitude of change was greatest in warmer areas, shallow water fish assemblages in cooler regions also shifted significantly, with little indication that assemblages are reverting to pre-heatwave states; instead, many SWA shallow reef assemblages appear to be settling into novel, persistent configurations. We further extended sampling to deeper reefs (35-70m) in 2023 using ROVs, to investigate whether depth buffers climate impacts on fish assemblages. Depth was a dominant structuring factor, and while species richness and abundance declined with depth, functional group composition overlapped substantially with shallow reefs. Evidence of deep-water recruitment for several species suggests potential for replenishing shallow populations. However, deep-water recruitment is likely depended on the thermal affinity of species and regional temperature regimes. Deeper reefs, particularly in cooler regions, showed signs of temporal stability indicating potential partial refuge from climate change. Together, these findings demonstrate how warming and marine heatwaves are reshaping shallow water reef fish communities and ecosystem functioning in a global hotspot, while highlighting depth as a partial, species-dependent buffer.