This work focused on the knowledge-based methodology for the development of an electrochemical system, enabling simultaneous optimization of various operating parameters such as current density (j), initial dye concentration (Co), NaCl concentration (CN) for the mineralization of Reactive Violet 2 (RV-2) and Acid Brown 14 (AB-14) dye on the efficiency of removal, energy consumption (EC), Chemical Oxygen Demands (COD), apparent rate constants (kapp) and Electrical Energy per Order (EEO) all of which have been examined. The relationship between kapp and EEO is also discussed. The degradation efficiency and kapp always rising at higher j and lower Co and CN while EC, EEO, and operating cost increased at higher j, Co and CN. On the other hand, The COD increased with decrease j, Co and higher CN. Due to the strong formation of hydroxyl radicals from water discharge, the graphite electrode possesses a strong power of electro-generation rate and competitive wasting reactions of organic compounds. The results demonstrated that the relatively high dye removal, COD and low specific energy consumption are obtained simultaneously only if the various parameters are regulated to a plausible value j of 79Am-2, Co of 100mg/L and CN of 1g/L within 60min of electrolysis. The color removal efficiency is much faster for RV-2 compared to AB-14 due to the contribution of azo bond in the dye molecule. Also, the EC and kapp are higher for RV-2 than AB-14 while is lower in terms of EEO and COD. A comprehensive reaction sequence of RV-2 and AB-14 mineralization involving all oxidation products was proposed. Formation and evolution of aromatic and aliphatic (short-chain carboxylic acids) intermediates during the treatment and a mineralization pathway is proposed. The estimated cost of operation for degradation at optimum conditions is calculated as 1.54 and 1.29 USD m-3/g dye for complete degradation RV-2 and AB-14, respectively.