The aim of the work was to develop novel green high-performance membranes based on sodium alginate (SA) with improved characteristics for pervaporation dehydration by bulk and surface modifications. Water-soluble fullerene derivatives (fullerenol and fullerene derivative with L-arginine) were used as modifiers for the bulk modification of sodium alginate matrix. Surface modification of developed SA membranes was carried out by the layer-by-layer assembly for the deposition of nanosized polyelectrolyte layers. The structural features and physicochemical properties of the composites and membranes was studied by various analysis methods: FTIR and NMR spectroscopies, scanning electron (SEM) and atomic force (AFM) microscopies, thermogravimetric analysis, measurements of contact angle and swelling experiments. Transport properties of the obtained membranes were evaluated in pervaporation dehydration of isopropanol in a wide concentration range. It was demonstrated that the combination of both bulk and surface modifications for SA membranes significantly improved transport characteristics.