Desalination by capacitive deionization (CDI) is a promising technique to combine desalination and energy storage. The efficiency of charge storage process, which is equivalent to the desalination process, depends strongly on the presence of Faradic side reactions on the electrode. Herein, the performance of a new low‐cost designed flow‐through electrode with porous carbon nanoparticles (CP) coating on carbon‐fiber paper (CFP) is evaluated. The CP layer enables high capacitance while the CFP core makes fluid dynamics along and across the electrode. The electrodes are evaluated by studying the effective operational CDI parameters, such as operational voltage, degassing of electrolyte, and salt concentration. The Faradic side reaction and its effect on charge efficiency (CE) are evaluated which are estimated to decrease to 46% by liquid flow bringing dissolved oxygen from the air‐electrolyte interface to the electrode. The CE enhances to 59% with a salt concentration of 1 m. By purging N2 gas, CE is much higher (>85%) with a maximum efficiency of 97% at 0.6 V. Three regimes of the complex kinetic of side reactions are found involving various species such as O2, H2O2, H2, and carbon oxidation and the implication of those regimes for real applications are discussed.