Harmful algal blooms (HABs) can have serious detrimental and economical on coastal ecosystems, industries, and communities. Globally, the spatial extent and frequency of HABs has increased significantly over the last 20 years. Whilst research has shown multiple causative factors contribute to the formation of HABs (e.g., eutrophication, water flow modifications, climate change) our lack of understanding of the interplay of these factors in HAB formation has made HAB prediction difficult. Here we show initial results of a novel fluorometer designed to detect HAB species. The fluorometer uses the differences in the fluorescence emission spectra to detect the presence of two HAB species Karenia mikimotoi and Chattonella marina. We integrated the fluorometer into the AquaWatch water quality monitoring system which is currently deployed in the coastal waters of Port Lincoln, home to South Australia’s highly valued fisheries and aquaculture industries. a history of Karenia mikimotoi blooms. The HAB fluorometer provides for the real-time detection of HAB species, and early validation against cell counts indicate the fluorometer has potential to provide reliable estimates of cell abundances. We demonstrate how integration of real-time detection capabilities with a nowcast/forecast hydrodynamic model can be used to predict HAB trajectories to help mitigate HAB bloom impacts on surrounding industries.