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In this study, an original use of immersed microfiltration membranes (mean pore size equal to 0.2 μm) is investigated for the total removal of toxic dinoflagellates from seawater. Using a membrane autopsy and fouling model approach and the use of fouling indexes (called Pore Blocking Index, Pore Constriction Index and Cake Filtration Index), three dinoflagellate suspensions (Heterocapsa triquetra, Alexandrium minutum and Prorocentrum lima) have been microfiltered in order to study the influence of micro-algal species and its concentrations (1,000 and 30,000 cells/mL) on filtration yield and membrane fouling mechanisms. Results showed that all micro-algae have been retained after 180 min of microfiltration. At 30,000 cells/mL, permeate fluxes declined rapidly and an internal fouling occurred at the beginning of microfiltrations followed by a cake deposition. At 1,000 cells/mL, flux declined slowly and was mainly due to an internal fouling. For a given micro-algae concentration, the filtration behaviour and fouling behaviour can be very different based on the micro-algae species. The dissolved organic substances and particulate size distribution are important factors affecting internal but also external fouling. SEM analyses and fouling indexes are useful tools, simple to implement, and allow the study of membrane fouling and membrane process optimization. Research highlights : ► Removal of toxic dinoflagellates from seawater using a low energy consumption membrane process. ► Microfiltration for safe shellfish storage during toxic micro-algae bloom. ► Retention of 99% of micro-algae by immersed microfiltration membrane. ► Understanding of membrane fouling mechanisms to process optimization.