The benefits provided by a model of system dynamics are directly related to its correct construction. One of the main challenges in the process of building such models is that they must be able to effectively represent a specific problematic situation. Thus, the main objective of this study is to develop a multi-methodological approach, adapting the problem structuring method of strategic options development and analysis (SODA) in the initial stage of the system dynamics (SD) model. The role of each of them clearly represents the contribution of this study: the SODA in the structuring (representation) phase of the problem and proposition of alternatives and the SD in the evaluation phase of these alternatives. To illustrate its application, the multimethodological approach developed was used to simulate scenarios considering management strategies, and the various variables affecting a water supply system, including population growth, in order to evaluate more “assertive” water management strategy(s) that could have been adopted to address the water crisis (2012–2017) and analysis future scenarios. The results show that, based on the vision of specialists with enough experience for the case studied, it was possible to structure the problem, and therefore propose a set of strategies (alternatives), which were: water loss control, wastewater reuse, application of more efficient tariffs to reduce water waste, inter-basin water transfer, and awareness regarding the use of water resources. After the survey of alternatives, scenarios were simulated considering these water management strategies. Simulation results showed that actions taken on the demand side would only be effective for a short period of water scarcity, (for example, the impact of the scarcity-based tariff on water consumption reduction). For severe drought scenarios and with a water producing system heavily dependent on rainfall, such action would no longer be efficient. However, water supply management-oriented strategies, e.g., inter-basin water transfers (PISF) and wastewater reuse, are highly effective in securing water supply and preventing water supply collapse in the region. The development of this multi-methodological approach is expected to be useful to support managers in the decision-making and implementation of water management strategies.