Karst hydrosystems represent one of the largest global drinking water resources, but they are extremely vulnerable to pollution. Climate change, high population density, intensive industrial, and agricultural activities are the principal causes of deterioration, both in terms of quality and quantity, of these resources. Samples from 172 natural karst springs were collected in the whole territory of Greece. To identify any geogenic contamination and/or anthropogenic pollution, analyses of their chemical compositions, in terms of major ions and trace elements, were performed and compared to the EU limits for drinking water. Based on chloride content, the collected karst springs were divided into two groups: low-chloride (< 100 mg L−1) and high-chloride content (> 100 mg L−1). An additional group of springs with calcium-sulfate composition was recognised. Nitrate concentrations were always below the EU limit (50 mg L−1), although some springs presented elevated concentrations. High contents in terms of trace elements, such as B, Sr, As, and Pb, sometimes exceeding the limits, were rarely found. The Greek karst waters can still be considered a good quality resource both for human consumption and for agriculture. The main issues derive from seawater intrusion in the aquifers along the coasts. Moreover, the main anthropogenic pollutant is nitrate, found in higher concentrations mostly in the same coastal areas where human activities are concentrated. Finally, high levels of potentially harmful trace elements (e.g. As, Se) are very limited and of natural origin (geothermal activity, ore deposits, etc.).