In this study, double‐layer flat sheet membranes consist of nanocomposite polyvinylidene fluoride (PVDF)–ZnO layer on the top, whereas pristine polymeric PVDF on the bottom was fabricated via the double‐casting phase inversion (DCPI) method. The nanocomposite layer was prepared by loading 0.5%, 1.0%, 1.5% and 2.0% of ZnO nanoparticles. The morphology of the membranes changed as ZnO nanoparticles were introduced in the top layer, where the structure is more rigid and porous than the bottom layer. The increment concentration of nanoparticles in the top layer of the double‐layer membrane gives an effect in increasing of water contact angle slightly, which is from 136° to 140°. Furthermore, the liquid entry pressure of water (LEPw) decreases gradually from 0.69 to 0.4 bar with a high concentration of ZnO due to the presence of large pores. The increment concentration of ZnO nanoparticles also resulted in high porosity and reduced pore size, which reduce the resistance of water vapour to pass through the pores as well as enhancing the performance of membrane distillation (MD). Direct contact membrane distillation (DCMD) experiments were carried out to evaluate the efficiency of the fabricated double‐layer membrane in the desalination of seawater from fish farm water for 6‐h operation. The optimal double‐layer membrane with 0.5% ZnO nanoparticles loading maintained a stable flux of 9.42 L/m2h with 99.9% salt rejection and has antifouling properties. The results indicated that the fabricated double‐layer membrane via the DCPI method fulfils the required properties for MD application with excellent salt rejection.