Inorganic-polymer hybrid, thinfilm nanocomposite nanofiltration (TFN-NF) membranes prepared by in situ interfacial polymerization of branched polyethyleneimine and trimesoyl chloride, with simultaneous impregnation of as-synthesized hexagonal wurtzite ZnO nanocrystals (nano-ZnO), either through aqueous or organic phase, have been extensively characterized. XPS analysis revealed that there was no inter-atomic charge transfer between nano-ZnO and host polyamide matrix, indicating that no formation of chemical bonding occurred between them in the skin layers of the membranes. The type of interaction present within the nanocomposite polyamide matrices of the membranes was through formation of noncovalent type secondary chemical interactions with peripheral hydroxyl groups of nano-ZnO and polyamide network as substantiated through FTIR analysis. SEM revealed the formation of distinct patterns and coils, through multiple-point interactions between the nano-ZnO and the polyamide network in the membranes' skin surfaces when introduced through aqueous amine phase. However, when introduced through the organic phase, nanomaterials remained distributed as discrete clusters within the membranes' skin layers because of lack of polar environment around the reaction zone, further emphasizing the role of the medium in which the nanomaterials are incorporated. AFM showed variation of surface roughness features with change in the precursor medium of introduced nano-ZnO. Nanofiltration performance towards different solutes, providing differential rejections in the order of MgCl2 > NaCl ≥ Na2SO4, revealed that the membranes were distinctly positively charged. Solvent fluxes of the membranes were significantly higher when nanomaterials were introduced through the aqueous phase as compared to the organic phase. © The Royal Society of Chemistry 2015.