Optimizing the design of water distribution systems often faces difficulties due to continuous variations in water demands, pressure requirements, and disinfectant concentrations. The complexity of this optimization even increases when trying to optimize both the hydraulic and the water quality design models. Most of the previous works in the literature did not investigate the linkage between both models, either by combining them into one general model or by selecting any representative solution to proceed from one model to another. This work introduces an integrated two-step framework to optimize both designs while investigating the reasonable network configuration selection from the hydraulic design view before proceeding to the water quality design. The framework is mainly based on a modified version of the multi-objective particle swarm optimization algorithm. The algorithm’s first step is optimizing the hydraulic design of the network by minimizing the system’s capital cost while maximizing the system’s reliability. The second step targets optimizing the water quality design by minimizing both the total consumed chlorine mass and the accumulated differences between actual and maximum chlorine concentrations for all the network junctions. The framework is applied to Safi Network in Yemen. Three scenarios of the water quality design are proposed based on the selected decision variables. The results show a superior performance of the first scenario, based on optimized 24-h multipliers of a chlorine pattern for a flow-paced booster station, compared to the other scenarios in terms of the diversity of final solutions.