Groundwater is an important resource for many countries and its scarcity is a major concern in small territories, especially in the islands where the constant extraction is creating a high risk of public calamity. This issue has been increasing because of the anthropogenic activities and the climate change and it has called the attention of scientists and stakeholders in order to assess the sustainability of the water management system, and therefore, to establish strategies for a more sustainable water use. San Andres island was taking as case study and a description of the water balance was carried out in order to understand the management system. Then, a water system sustainability assessment was performed with indicators such as water security, water quality, drinking water, sanitation, infrastructure, climate robustness, biodiversity, attractiveness, and governance, according to the City Blueprint Methodology. The result for the 24 evaluated indicators was a score of 3.2, whose interpretation is “an unsustainable water management”. The qualitative assessment was the base to propose water security, water quality, and governance strategies to improve the water management in the island. The assessment and its discussions are relevant for the water management in small islands across the world whose economy is based on the tourism and whose water security is at a high risk.