This work presents a detailed investigation into the long term stability of polyelectrolyte multilayer (PEM) modified membranes, a key factor for the application of these membranes in water purification processes. Although PEM modified membranes have been frequently investigated, their long term stability, critical for application, has not been considered up till now. We focus on both the physical stability of the multilayer on different membranes as well as on the chemical degradation of two different multilayers in the presence of sodium hypochlorite. Two different polymeric ultrafiltration membranes are modified to become dense nanofiltration membranes by applying a thin (PEM) coating on the membrane via the Layer-by-Layer technique. During sequential backwash cycles, no performance loss is observed for PEM modified membranes based on sulfonated poly(ether sulfone) (SPES). On the other hand, PEM modified membranes based on the non-ionic poly(ether sulfone) (PES) show a gradual increase in permeability and loss in retention after each backwash cycle. We demonstrate that a PEM on an ultrafiltration membrane that bears ionic charges has superior adhesion to the substrate, ensuring long term stability. In addition, the chemical stability of two different multilayers is assessed by means of the resistance against sodium hypochlorite degradation. An important factor in the chemical stability is the type of polycation. Membranes coated with multilayers based on the primary polycation poly(allylamine) hydrochloride (PAH) show a loss in performance after 24,000 ppm hours NaOCl (pH 8). Membranes coated with multilayers based on the quaternary polycation poly(diallyldimethylammonium) chloride (PDADMAC) are stable for more than 100,000 ppm hours NaOCl (pH 8), which is an excellent stability, comparable to that of commercial PES ultra- and microfiltration membranes.