Seagrasses are key marine habitats that are increasingly degraded globally due to anthropogenic disturbances and climate change, compromising the ecosystem services they provide. While seagrass loss is often patchy, the ecological consequences of meadow fragmentation on marine fauna remains unclear. This study quantified decadal change in seagrass habitat and fragmentation of the globally important meadows of the Shark Bay World Heritage Area following the 2011 marine heatwave (MHW) and assessed how meadow structure and fragmentation influence fish assemblages. In situ seagrass data were integrated with seascape metrics derived from habitat maps generated from satellite imagery to characterise temporal changes in meadow structure. Seagrass data and seascape metrics were related to fish abundance, diversity and productivity using fish data collected from trawls and unbaited remote underwater video (URUV). A temporal lag in dense seagrass loss (1382 Ha) occurred approximately six years post-MHW, with an increase in sparse patches indicating fragmentation. Greater cover of seagrass at the local meadow scale (~ 50 m2) positively influenced the abundance, biomass, and net productivity of small-bodied fishes collected in trawls. The high structural complexity of Amphibolis antarctica dominated meadows also benefitted small-bodied fishes. URUVs recorded more large-bodied, mobile fishes near channels, possibly reflecting the importance of these areas facilitating habitat connectivity of adult fishes. Canopy-forming seagrass habitats are important for fish communities, and MHWs may impact small-bodied fishes via reductions in seagrass cover. These findings support management approaches that prioritise the conservation of patch connectivity and high seagrass cover in shallow coastal systems.