Among all the techniques studied to overcome fouling generated in dead-end filtration, the injection of air during backwashes proved to be the most effective. Indeed, shear stress engendered by the two-phase flow enhanced particle removal on membrane surface. This work aims to study the injection of air to drain the membranes before backwash. Firstly, the efficiency of this backwash procedure was evaluated during the ultrafiltration of seawater on a semi industrial pilot plant using different operating conditions. Then, the treatment of seawater, doped with oyster gametes to simulate the filtration of shellfish hatchery effluents, was performed to confirm the hydraulic performance of the air backwash. Indeed, the release of gametes, expulsed by exotic bivalves in the natural environment, could be a risk for the biodiversity preservation. The impact of air backwash on the integrity of oocytes and spermatozoa was identified using flow cytometry and microscopic analyses. When oyster gametes were added, their retention by ultrafiltration was validated. The impact of air backwash on these species viability was a significant information point for the implementation of this process on shellfish production farms.