Abstract Two crosslinking methods for layer-by-layer (LbL)-assembled nanofiltration membranes were developed to improve the stability of the membrane under high ionic strength conditions and chlorine treatment. In the first method, an amine coupling reaction was applied between amino groups on cationic polyelectrolytes and carboxyl groups on anionic polyelectrolytes. The amine coupling reaction was carried out by an active ester method using 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide, and crosslinked LbL membranes via amide bond formation. The crosslinking by amine coupling reaction improved the stability of the membrane performance under high ionic strength conditions. However, it was not effective under chlorine treatment. As a next challenge, we crosslinked LbL membranes by a silane coupling reaction between oppositely charged polyelectrolytes modified with reactive silane groups. Cationic and anionic polyelectrolytes modified with reactive silane groups were synthesized, and the synthesis of the polyelectrolytes was confirmed by Fourier transform infrared spectroscopy. The LbL membranes were fabricated with the synthesized polyelectrolytes and crosslinked via siloxane bond formation between oppositely charged polyelectrolytes. The silane coupling reaction improved the separation performance of the membranes, and the siloxane-crosslinked membranes were found to be highly stable under both high ionic strength conditions and chlorine treatment.