This study addresses complex multi-objective optimization challenges in large-scale, real-world water distribution networks (WDNs). The primary objectives are to improve a water quality index (water age) and network resilience by optimizing pipe diameters and network topology as decision variables. The proposed approaches leverage the non-dominated sorting genetic algorithm II (NSGA-II) producing Pareto optimal alternatives for water utility decision-makers. To enhance computational convergence runtime and solution quality of optimization, novel techniques are employed. These include advanced NSGA-II constraint handling, search space reduction, graph theory-based formulation of decision variables, constraints, and objective functions, as well as multi-stage and hydraulic-free optimization strategies. Furthermore, soft constraints are relaxed and integrated into Pareto decision-making spaces to provide a comprehensive, multi-criteria decision-making framework. The approaches are applied to a real case study, and the results demonstrate optimization performance improvements, with efficiency increasing by approximately 20% (in terms of convergence speed). Additionally, water age is reduced by 52% while achieving favorable results in the hydraulic and topological criteria. These findings highlight the effectiveness of the proposed methodologies in addressing WDN optimization challenges.