Alternating deposition of oppositely charged polyelectrolytes (PEs) can create stable solvent resistant nanofiltration (SRNF) membranes with very high flux and selectivity. Combinations of poly(diallyldimethylammonium chloride) (PDDA) as polycation and poly(sodium styrene sulfonate) (PSS) or poly(vinyl sulfate) (PVS) as polyanions are reported from which supported membranes consisting of 5, 10, 15 and 20 bilayers are prepared via the layer-by-layer (LBL) method. The morphology of membranes prepared with polyanions in the Na- and H-form was studied by SEM and AFM. Membranes were applied in the filtration of organic solvents. Substitution of the counterion in the polyanion solutions influenced the interaction between the ions and the PE and consequently changed the PE conformation and the properties of the PEC films. The membranes prepared from polyanions in the H-form showed higher permeabilities and higher retentions than the ones prepared from the Na-form. All membranes showed very good retentions up to 99% for charged solutes in the pressure driven filtration of isopropanol (IPA) solutions and also showed excellent potential in the challenging polar aprotic solvents, such as N,N-dimethylformamide (DMF).