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Increasing urban water demand and water stress conditions due to population growth, combined with climate change and a non-uniform distribution of water resources in space and time, represent major concerns for water companies. As such, long-term management strategies need to improve the resilience of water supply systems and account for the sustainability of water withdrawals. In this context, metabolic modelling may provide a support to decision-making in the medium-long term, based on sustainability criteria. This approach enables mimicking a water supply network (WSN) based on a set of material and energy fluxes that interact and influence each other. By analyzing these fluxes, a suite of key performance indicators (KPIs) is evaluated in order to identify which kind of interventions may be applied to increase the sustainability of the system. Here, we apply a metabolic model, WaterMet(2), to a WSN in the Reggio Emilia Province (Italy), combined with hydraulic simulations conducted with EPANET. Different alternative strategies are compared, including a reduction of water withdrawals from the main well field due to a possible future decrease in water availability. Based on KPIs, sustainable long-term strategies are evaluated in order to identify the most suitable solution for dynamic sustainable management of the water supply system.