The sustainability of the water supply program in developing countries is influenced by many inter-linked and dynamic factors, suggesting the need to analyse the system behaviour of the water supply program. However, no study analyses factors influencing the sustainability of rural drinking water supply programs holistically, and this study aims to fill that gap. This study utilized a system dynamics approach based on a case study of a community-based rural drinking water supply program (PAMSIMAS in Bahasa) in Magelang Regency, Indonesia. Five sustainability aspects were considered in the model development and simulation: Financial, institutional, environmental, technical, and social aspects. Eight scenario analyses related to those five aspects were conducted. The causal loop diagrams suggest that the overall loop in the system is reinforcing, meaning that the improvement in one aspect will improve the overall condition of the system and deterioration in one aspect will reduce the overall condition of the system. Scenario analysis shows that external fund is critical to support the program financially, especially at the beginning of the project when the piped system is being built and water revenue is still low. Scenario and sensitivity analyses revealed that human factors, i.e., the performance of the water board and response and support from the community, positively influence the sustainability of the water supply program. Additionally, the water board plays a key role in accelerating the pipe network growth. Finally, this paper argues that visualising and simulating the causal relationship and dynamic behaviour of the rural water supply program are critical for water stakeholders to better design and implement the water supply program.