Globally, water quality indices (WQIs) are beneficial for evaluating groundwater and surface water quality. The Canadian Council of Ministers of Environment Water Quality Index (CCME WQI) was combined with the parametric values given by Directive 98/83/EC to investigate the possible suitability of groundwater resources for human consumption on Rhodes Island. Chloride (Cl−), pH, calcium (Ca2+), electrical conductivity (CND), carbonate (CO32−), bicarbonate (HCO3−), potassium (K+), magnesium (Mg2+), sulfate (SO42−), sodium (Na+),nitrate (NO3−), nitrite (NO2−), ammonium (NH4+), and phosphate (PO43−) were included in the dataset applied in this study. Statistical analysis, GIS database, and WQI estimation were successfully used to evaluate the groundwater resources of the study area. All studied groundwater parameters have mean and median values lower than the corresponding parametric values established by Directive 98/83/EC. The high CND values (up to 2730 μs cm−1) in groundwater collected from Rhodes’ coastal aquifers indicate a direct relationship with seawater intrusion. CCME-WQI classifies the groundwater samples for most monitoring stations on Rhodes aquifers as “excellent”, Class 5, for 2019 and 2020. The findings of this study may be helpful for scientists and stakeholders monitoring the study area and applying measures to protect the groundwater resources.