Human pressures accumulating on the marine environment, and among the different impacts, pollution, such as that caused by pesticides, is known to jeopardize the shellfish life cycle. The SOAP (Securing shellfish hatcheries by coupling processes) project aimed to improve safety in shellfish hatcheries through the development of an innovative seawater treatment combining ultrafiltration (UF) and activated carbon (AC) processes for the disinfection and chemical decontamination of seawater. The main objectives were to (i) identify the organic micropollutants (OMP) present in coastal seawater, (ii) select optimal treatment conditions to remove these molecules, (iii) study the impact of water quality, after treatment by UF and UF + AC, on shellfish (oyster Magallana gigas and clams Ruditapes philippinarum) and microalgae feed production, and (iv) transfer the best processes to industrial partner sites to evaluate their performance under real conditions (industrial scale with real seawater). Oyster fertilization tests showed high performance of the processes (UF + granular AC or powdered AC) to treat seawater spiked with micropollutants and hatching rates obtained were similar or even higher than the control (sand filtration 30 mu m and UV-disinfected seawater). At the industrial scale, UF enabled to retain bacteria and the combination with granular AC confirmed the efficiency to remove the chemical pollution present in seawater, thus protecting the shellfish and microalgae produced in treated water. However, possible contamination after UF in pipes or AC must be considered. Regarding the microalgae production for feeding clams, UF without granular AC yielded the best results in terms of ease of use and of production. In real conditions, for 1 year, the UF pilot plant proved its robustness and viability, regardless of seawater quality or the operating conditions imposed by the industrial partners. UF-AC seawater treatment process appears to be efficient for the removal of micropollutants and mollusk pathogens.