Solution-processable polyelectrolyte complex (PEC) modified with various water-soluble fullerene derivatives (fullerenol, carboxyfullerene, fullerene derivative with L-arginine) were synthesized by using sodium carboxymethyl cellulose (CMC) and poly(diallyldimethylammonium chloride) (PDADMAC) for the creation of novel supported mixed matrix membranes for enhanced pervaporation and nanofiltration. The optimal preparation conditions and membrane composition were found. The structural characteristics and physicochemical properties of PEC-based membranes were analysed by Fourier-transform infrared (FTIR) spectroscopy, X-ray photoelectron spectroscopy (XPS), scanning electron (SEM) and atomic force (AFM) microscopies, thermogravimetric analysis (TGA), contact angle measurements and swelling experiments. The developed membranes were tested in pervaporation dehydration of isopropanol (12–50 wt% water) and, for the first time, in nanofiltration of heavy metals (model solutions and wastewater from galvanic production). Optimal transport characteristics were possessed by a supported membrane with a selective layer based on PEC-fullerenol (4%) composite: improved permeation flux of 0.28–1.62 kg/(m²h) and 99.99–79.30 wt% water in permeate in pervaporation dehydration of isopropanol (12–50 wt% water) at 22 °C, and 2.5 times improved permeability at a high rejection coefficients in nanofiltration of heavy metals compared to the pristine CMC membrane, which indicated its promise industrial application for water purification.