This research explores the strategic optimization of secondary chlorination in water distribution systems (WDSs), in order to enhance the efficiency of disinfection while mitigating odor and operational costs and promoting sustainability in water quality management. The methodology integrates EPANET simulations for water hydraulic and quality modeling with a deep belief network (DBN) within the deep learning framework for accurate chloric odor prediction. Utilizing the non-dominated sorting genetic algorithm-II (NSGA-II), this methodology systematically balances the objectives of chloride dosage and chloramine formation. It combines a chloric odor intensity assessment, a multi-component kinetic model, and dual-objective optimization to conduct a comparative analysis of case studies on secondary chlorination strategies. The optimal configuration with five secondary chlorination stations reduced chloric odor intensity to 1.20 at a cost of USD 40,020.77 per year in Network A while, with eight stations, chloric odor intensity was reduced to 0.88 at a cost of USD 71,405.38 per year in Network B. The results demonstrate a balanced trade-off between odor intensity and operational cost on one hand and sustainability on the other hand, highlighting the importance of precise chlorine management to improve both the sensory and safety qualities of drinking water while ensuring the sustainable use and management of water resources.