Long-term sustainability in water supply systems is a major challenge due to water resources depletion, climate change and population growth. This paper presents a scenario-based approach for performance assessment of intervention strategies in water resources and supply systems (WRSS). A system dynamics (SD) approach is used for modelling the key WRSS components and their complex interactions with natural and human systems and is combined with a multi-criteria decision analysis for sustainability performance assessment of strategies in each scenario. The scenarios combine population growth rates with groundwater extraction limits and three intervention strategies. The methodology was demonstrated on a real-world case study in Iran. Results show scenario-based analysis can provide suitable strategies leading to long-term sustainability of water resources for each scenario imposed on the water systems. For scenarios with either no threshold or one threshold of groundwater extraction limit, the only effective strategies for sustainable groundwater preservation are those involving agricultural water demand decrease with an average recovery rate of 130% for groundwater resources while other strategies of agricultural groundwater abstraction (constant/increase rates) fail to sustainably recover groundwater resources. However, all analysed strategies can provide sustainability of water resources with an average recovery rate of 33% for groundwater resources only when scenarios with two threshold limits are in place. The impact of scenarios on groundwater conservation is quite minor for population growth rates with an average recovery rate of 11% compared to groundwater extraction limits with an average recovery rate of 79% between no threshold and two threshold limits.