Layer by layer (LBL) hollow fiber nanofiltration (NF) membranes assembled by poly(styrene sulfonate) (PSS)/poly(allylamine) (PAH) with 2.5 bilayers, both uncrosslinked (PSS/PAH)2.5 and crosslinked (PSS/PAH)2.5-X, were researched as a pretreatment for seawater. Focusing on the stability and ion rejections, PSS/PAH NF membrane demonstrated long time stable ion rejection after exposure in artificial seawater (ASW, >300 h) and a unique ion rejection behavior. Overcompensation of PAH contributed to the excess cationic amine groups in LBL layers. This explains the high rejection of bivalent cations, Mg2+, Ca2+ and Sr2+, for both membranes size exclusion and Donnan effect for single salt feed. The extrinsic compensation of SO42− to cationic amine groups for (PSS/PAH)2.5 resulted in unexpected lower rejection of SO42− than Cl−. In ASW, increased rejection to SO42− and reduced rejection to Cl−, bivalent and monovalent cations caused by the extrinsic compensation of Cl− to the amine groups highlighted the dominance of the affinity or sorption effect over the size and Donnan effect. A coherent ion rejection mechanism incorporating anion extrinsic compensation, combined with the size and Donnan exclusion, constitutes the third dimension for ion transport across LBL membranes.