Harmful algal blooms (HAB) are increasing worldwide, including across Australia’s Great Southern Reef, causing mass mortalities of marine life and economic loss. To investigate the effect of harmful algae bloom on the ocean microbiome we collected a monthly time series (since March 2025) via the water column using metagenomics and flow cytometry, at 6 locations (3 independent samples each) across the Great Southern Reef. Our preliminary data shows a 6-fold increase in microbial abundance with high abundance of Karenia spp. suggesting microbes are enhancing dinoflagellate growth. A subset of the microbiomes was sequenced on the Nanopore promethION (28 samples 1,089,171 reads 278,245,169 bp average 38,899 reads and 9,937,327 bp per sample) to provide a high-resolution view of both the holobiont community composition and metabolic potential across space and time during the bloom. We aggregated all taxa annotated as Dinophyceae, and correlated with the microbiome, which revealed a consistent ecological signal. Dinophyceae abundance was positively associated with marine copiotrophic taxa, including Flavobacteriia (e.g. Winogradskyella), Gammaproteobacteria (e.g. Enterovibrio, Pseudoalteromonas). Conversely, Dinophyceae abundance was negatively associated with oligotrophic taxa and competing phytoplankton lineages (e.g. green algae such as Micromonas and Ostreococcus), indicating a shift from a nutrient-limited baseline community to a bloom-associated, resource-rich ecosystem. Notably the preliminary analysis identified that there was a rise in cell-division-associated functions that consistently precedes or coincides with early increases in Dinophyceae, supporting the hypothesis that microbial community activation is an early indicator, and potentially a driver of bloom formation.