The present paper aims to address the sustainable management issues of karst water sources in Slovenia and Croatia. It focuses on the Mediterranean part of the Dinaric karst, which holds important groundwater reserves. The importance of selected karst aquifers for water supply is presented. In addition, national drinking water management strategies are examined to synthesise the issues relating to the exposure of groundwater to contamination and over-exploitation. Finally, the most significant problems, pressing needs and challenges are identified. These depend predominantly on revision of existing drinking water protection strategies and integration of karst-specific provisions, aspects of over-exploitation and proper water quality control. The need for harmonised multi-country policies regulating resource abstraction and contamination issues is stressed.