Freshwater resource availability in SIDS, including Mauritius, is on the verge of becoming a major constraint to socio-economic development. A freshwater vulnerability assessment was undertaken for the period of 2000–2015 to understand the present vulnerability of the water systems in Mauritius and a future vulnerability estimation. Currently, the freshwater sector has been classified as a moderately vulnerable sector with a Freshwater Vulnerability Index (FVI) of 0.36–0.38 derived from a resource availability of 1091–1184 m3/capita, a coefficient of rainfall variation of 0.206–0.220, a water exploitation rate of 72–76% and ecological degradation of 30–39% for the period of 2000–2015. For the period of 2020–2050 under a business as usual scenario, the freshwater sector remained in a moderate-vulnerability region whereby the water exploitation rate was found to be the most affected vulnerability parameter with an increase to 95% exploitation by 2050. Under the effects of climate change, the FVI increased to a range of 0.38–0.44 indicating a shift from moderate- to high-vulnerability region and the findings also indicate that the country is likely to enter into a water scarcity region (water availability of < 1000 m3/capita) by 2030 and face overexploitation of water resources (water exploitation rate > 100%) by 2040. For all three scenarios, the resource stress category showed the highest contribution on the calculated FVI with a share of contribution of 33–38% to the current FVI, 34–38% to the predicted FVI for a business as usual scenario and 40–43% to the predicted FVI under the effects of climate change.