Spencer Gulf, southern Australia, is a highly productive coastal system where water quality is tightly linked to phytoplankton dynamics and ecosystem health. Rising ocean temperatures associated with climate change are placing increasing pressure on marine environments, potentially driving shifts in phytoplankton community composition and the emergence of harmful algal blooms (HABs). This study examines the influence of environmental variables on phytoplankton communities in Spencer Gulf using pigment composition as a diagnostic indicator of water quality change between 2022 and 2024. Distinct seasonal patterns were observed, with diatoms and haptophytes dominating in late spring and early summer, green algae in late winter, type 1 dinoflagellates during summer and autumn, and type 2 dinoflagellates in autumn and mid‑winter. Notably, gyroxanthin diester, 4‑keto‑19‑hexanoyloxyfucoxanthin, and three fucoxanthin derivatives associated with Karenia (type 2 dinoflagellates) were detected in May and July 2023 and May 2024. These HAB‑related pigments showed strong positive correlations with the organic fraction of total suspended solids. Elevated chlorophyll‑a concentrations were also recorded during these periods, with a clear increase from 2023 to 2024. CDOM absorption (ag412) was also observed to be comparatively high during this time. The detection of HAB‑associated pigments highlights the need for sustained bio‑optical monitoring to identify bloom drivers and mitigate impacts on water quality.