Poly(ether imide) (PEI) ultrafiltration membranes were chemically modified with branched poly(ethyleneimine) to obtain nanofiltration (NF) membrane Cat PEI with a positive charge in the pH range below 9. An oppositely charged polyelectrolyte layer was deposited on the resulting membrane surface by using sodium polystyrene sulfonate (PSSNa) and sodium polyvinyl sulfonate (PVSNa) to prepare a bipolar layered membrane NF Cat PEI_PSS and Cat PEI_PVS having a negatively charged surface and positively charged pores. Cat PEI exhibited good performance to remove multivalent cations (more than 90% of Ca2+) from single salt solutions except in presence of sulfate ions. Adding an anionic polyelectrolyte layer onto the positively charged surface resulted in a significant enhancement of rejection performance even in presence of sulfate anions. Application of the prepared membranes in water softening of natural complex mixtures was successful for the different studied membranes and a large decrease of hardness was obtained. Moreover, Cat PEI_PSS showed a good selectivity for nitrate removal. Fouling experiments were carried out with bovine serum albumin, as model protein foulant. Cat PEI_PSS showed much better fouling resistance than Cat PEI with a quantitative flux recovery ratio.