Harmful algal blooms (HABs) are emerging as increasingly important ecological disturbances in warming marine ecosystems, yet their effects on spatially discrete spawning aggregations remain poorly understood. In early 2025, Gulf St Vincent (GSV), South Australia, experienced an unprecedented HAB that persisted for more than 12 months and coincided with the austral summer spawning period of snapper (Chrysophrys auratus). Here, we assess changes in snapper biomass and spatial distribution at fixed, structure-associated spawning aggregation sites using repeated hydroacoustic–optical surveys conducted before (January 2025) and after (January 2026) the bloom peak. Across 32 paired benthic structures, total observed snapper biomass declined by 35%, although responses were spatially heterogeneous. Widespread biomass losses occurred across central, southern and western regions of GSV, while biomass increased sharply at a small number of northern structures, resulting in a markedly more concentrated spatial distribution in 2026. To investigate potential drivers of these changes, we compared survey results with independent datasets describing HAB intensity, temperature and prey distribution. Observed patterns were inconsistent with strong size-selective mortality and prey availability, weakly consistent with spatial variation in HAB intensity, but closely aligned with spatial thermal structure, suggesting redistribution toward preferred environmental conditions following disturbance. Our findings indicate that extreme events can simultaneously reduce local biomass and reorganise the spatial structure of fish populations, with potential consequences for spawning dynamics, ecosystem resilience and fisheries productivity. By treating fixed aggregation sites as ecological indicators, this study demonstrates the value of repeated ecosystem surveys for detecting and interpreting rapid ecological change in marine climate hotspots. As warming oceans increase the frequency and intensity of marine heatwaves, HABs and other ecosystem disturbances, sustained monitoring of key fish populations will be critical for tracking redistribution, identifying climate refugia, and supporting spatially explicit ecosystem-based fisheries management.