Nowadays, nanofiltration is actively used for water softening and disinfection, pre-treatment, nitrate, and color removal, in particular, for heavy metal ions removal from wastewater. In this regard, new, effective materials are required. In the present work, novel sustainable porous membranes from cellulose acetate (CA) and supported membranes consisting of CA porous substrate with a thin dense selective layer from carboxymethyl cellulose (CMC) modified with first-time synthesized Zn-based metal-organic frameworks (Zn(SEB), Zn(BDC)Si, Zn(BIM)) were developed to increase the efficiency of nanofiltration for the removal of heavy metal ions. Zn-based MOFs were characterized by sorption measurements, X-ray diffraction (XRD), and scanning electron microscopy (SEM). The obtained membranes were studied by the spectroscopic (FTIR), standard porosimetry and microscopic (SEM and AFM) methods, and contact angle measurement. The CA porous support was compared with other, prepared in the present work, porous substrates from poly(m-phenylene isophthalamide) and polyacrylonitrile. Membrane performance was tested in the nanofiltration of the model and real mixtures containing heavy metal ions. The improvement of the transport properties of the developed membranes was achieved through Zn-based MOF modification due to their porous structure, hydrophilic properties, and different particle shapes.