The entrance of even a small amount of phosphorus compounds into natural waters leads to global problems that require the use of modern purification technologies. This paper presents the results of testing a hybrid electrobaromembrane (EBM) method for the selective separation of Cl−(always present in phosphorus-containing waters) and H2PO4−anions. Separated ions of the same charge sign move in an electric field through the pores of a nanoporous membrane to the corresponding electrode, while a commensurate counter-convective flow in the pores is created by a pressure drop across the membrane. It has been shown that EBM technology provides high fluxes of ions being separated across the membrane as well as a high selectivity coefficient compared to other membrane methods. During the processing of solution containing 0.05 M NaCl and 0.05 M NaH2PO4, the flux of phosphates through a track-etched membrane can reach 0.29 mol/(m2×h). Another possibility for separation is the EBM extraction of chlorides from the solution. Its flux can reach 0.40 mol/(m2×h) through the track-etched membrane and 0.33 mol/(m2×h) through a porous aluminum membrane. The separation efficiency can be very high by using both the porous anodic alumina membrane with positive fixed charges and the track-etched membrane with negative fixed charges due to the possibility of directing the fluxes of separated ions in opposite sides.