Harmful algal blooms (HABs) can strongly affect marine fish populations, yet their effects on spatially discrete spawning aggregations remain poorly understood. In early 2025, Gulf St Vincent (GSV), South Australia, experienced an unprecedented HAB lasting more than 12 months, coinciding with the austral summer spawning period of snapper (Chrysophrys auratus). This study evaluates changes in snapper biomass and spatial distribution at fixed, structure‑associated 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%, with strong spatial heterogeneity. Substantial and consistent biomass losses occurred across central, southern, and western GSV, whereas biomass increased sharply at a small number of northern structures. This shift resulted in a more spatially concentrated distribution in 2026. Relationships with environmental datasets, including HAB intensity, temperature, and prey distribution, were examined. Patterns were inconsistent with strong size‑selective mortality and prey availability, and only weakly aligned with spatial variation in HAB intensity. In contrast, they closely matched thermal structure, suggesting redistribution toward preferred environmental conditions following disturbance. By treating fixed aggregation sites as ecological indicators, this study demonstrates how extreme events can both reduce biomass and reorganise distribution. Post‑disturbance concentration may increase vulnerability to depletion but also highlights critical refugia for recovery, supporting spatially explicit, ecosystem‑based fisheries management.