The process of ultrafiltration (UF) of natural seawater often encounters the problems of variation in water quality and coastal blooms. To validate the feasibility of UF in shellfish farms, this study compared the hydraulic performance and pollutant removal efficiency of the UF process with those of the commonly used treatments that combine several filtration steps with UV disinfection. The comparison was conducted in the cases of natural seawater and a coastal bloom. Given that the UF process encountered this specific pollution, this study evaluated the filtration performance of the UF process and the retention of total suspended solids (TSS), bacteria, phytoplankton, and zooplankton. A real coastal bloom was considered in the case study of an experimental shellfish hatchery/nursery in France. The results show that both treatments were able to eliminate approximately 50% of TSS. However, in contrast with UV treatment combined with filtration, the UF process retained total amounts of phytoplankton, zooplankton, and bacteria in the bloom. Although the hydraulic performance of the UF process was impacted by the coastal bloom, the fouling was eliminated through chemical cleaning conducted at a frequency less than once per 12 h. Despite the severe pollution, this study confirmed the pollution resistance and treatment performance of the UF process, indicating that UF has the potential to enhance the biosecurity level.