Sulfonated poly(ether ether ketone) (SPEEK), synthesized for use as a cation exchange polymer, and aminated polysulfone (APSf), synthesized for use as an anion exchange polymer, were applied to commercial carbon electrodes through direct coating. Then the flow pattern was investigated using a computational fluid dynamics (CFD) analysis to find any occurrence of dead zones in the existing cell. On the basis of the CFD analysis, new capacitive deionization (CDI) cells were designed to minimize the dead zones. Next, a comparison between the old and newly designed cells was conducted through CDI experiments to determine the ability of the newly designed cells equipped with SPEEK and APSf coated electrodes to separate NaCl, MgCl2, CaCl2, and MgSO4 under a variety of experimental conditions. Under the given experimental conditions, a salt removal efficiency (SRE) of 100% was generally obtained at cell voltages above 1.2 V. For single component seed solutions of NaCl, MgCl2, CaCl2, and MgSO4, the SRE was determined in the order of NaCl > MgCl2 > CaCl2 > MgSO4. In a case of city tap water, even with a low feed concentration of 70 mg/L, we were able to obtain an SRE of 92.3%, and this result was attributed to the larger number of multivalent metal ions in the feed compared with the number of monovalent ions.