To improve the process of ethanol dehydration via pervaporation, a molecular magnet [Fe4(acac)6(Br-mp)2] was synthesized and applied as a filler for hybrid alginate membranes and compared with membranes loaded with magnetite and Prussian blue. Synthesized powders and membranes were comprehensively characterized by means of FTIR spectroscopy, contact angle, degree of swelling, electron microscopy and magnetometry, to provide an extensive analysis of their physicochemical and magnetic properties. The results showed a strong correlation between filler properties and separation effectiveness, particularly flux. Consequently, the highest value of flux (25.46 kg∙m−2∙h−1) was achieved by an alginate membrane filled with magnetite. On the other hand, the value of separation factor was found to be the most beneficial in the case of membranes loaded with Prussian blue and a molecular magnet, which was associated with the hydrophilicity of the fillers, their compatibility and good distribution in a polymer matrix. Therefore, the most favourable results were obtained for alginate membranes containing 12 and 15 wt% of [Fe4(acac)6(Br-mp)2], where pervaporation separation index reached the value of 1261 and 1275 kg∙m−2∙h−1, respectively.