Coastal ecosystems are increasingly affected by human activities and climate change. These factors can alter the structure and functioning of phytoplankton assemblages, potentially favouring the development of Harmful Algal Blooms (HABs). Rising temperatures, changing nutrient regimes, and altered hydrodynamic conditions can modify species composition and promote the proliferation of bloom-forming, potentially toxic taxa. This has consequences for biodiversity, the trophic network, and the ecosystem services on which human activities, including shellfish farming, rely. In order to understand how phytoplankton respond to environmental disturbance, approaches are needed that can detect changes in community composition at an early stage of bloom development. In this context, integrating a recent, innovative molecular approach such as droplet digital PCR (ddPCR) into ecological monitoring programmes could provide a sensitive method of quantifying target phytoplankton species and detecting early changes in community composition. Direct estimates of rDNA copy number per cell, obtained without the use of internal standard curves, revealed significant variability among ecologically relevant taxa. This ranged from 4.65 copies cell⁻¹ in the bloom-forming diatom Skeletonema spp., to 5.58 copies cell⁻¹ in Chaetoceros socialis, and from 23 copies cell⁻¹ in the potentially toxic diatom Pseudo-nitzschia spp., to 7,845 copies cell⁻¹ in the toxic dinoflagellate Alexandrium minutum. These taxon-specific differences greatly improve the interpretation of molecular abundance estimates and facilitate the identification of ecologically meaningful changes in phytoplankton community structure in response to environmental disturbance. Furthermore, the timely detection and quantification of harmful taxa provide a basis for early warning systems and adaptive management strategies aimed at mitigating the ecological and socio-economic impacts of HABs. Integrating molecular indicators with ecological monitoring can support risk assessment and decision-making in mussel farming areas, thereby contributing to the preservation of the functioning of coastal ecosystems that are increasingly exposed to global change and the sustainable management of these ecosystems.