Within the framework of »Water Management Plan for the Danube River Basin and the Adriatic Sea 2015-2021 (NUV II)«, a study on the groundwater status of karst aquifers which are habitats of groundwater dependent ecosystems (GDEs) was carried out. Among them are the habitats of olms (Proteus anguinus), the endemic species of Dinaric karst. These habitats have been included in the Slovenian part of the Natura 2000 network, which aims at protecting and preserving rare, endangered and endemic animal and plant species and habitat types. However, the conservation status of some olm habitats is unfavourable given that the number of specimens is declining. For this purpose we prepared hydrogeological conceptual models, where recharge areas were delineated and quantitative as well as qualitative status of surface and ground-waters were studied. Knowing the basic characteristics of olms, their habitats and critical parameters that adversely affect their conservation status, we identified locations where critical parameters could exceed the threshold values in groundwater. We also identified the areas where and what are the trends of the observed parameters that exceed the natural background (As, Zn) or are undoubtedly of anthropogenic origin (PCB).