Emerging organic contaminants (EOCs) are a vast group of often (very)persistent, (very)mobile and toxic (PMT/vPvM) substances that are continuously released worldwide, posing environmental and human health risks. Research on occurrence and behavior of EOCs in karst is in its infancy, thus policy measures and legislative control of these compounds in groundwater are still lacking. The Dinaric karst aquifers are an essential source of drinking water for almost half of Croatia's territory. Intense karstification, complex heterogeneous characteristics, and high fracture-cavernous porosity result in rapid, far-reaching groundwater flow and large karst springs, but also high intrinsic vulnerability due to low contaminant attenuation. To prioritize future monitoring and establish appropriate thresholds for EOCs detected in Croatian karst drinking water resources, in silico tools based on quantitative structure-activity relationships were used in PBT (persistence, bioaccumulation, and toxicity) and PMT/vPvM analyzes, while toxicological assessment helped identify potential threats to human health. In 33 samples collected during two sampling campaigns in 2019 at 16 karst springs and one lake used for water supply, we detected 65 compounds (EOCs and some legacy chemicals), of which 7 were classified as potentially PBT or vPvB compounds (PFOS, PFHxS, PFHpA, PFOA, PFNA, boscalid, and azoxystrobin), while only 2 compounds were assessed as not PMT/vPvM. This finding underlines that most of detected EOCs potentially endanger karst (ground)water ecosystems and important drinking water sources in Croatia. Comparison of maximum concentrations with existing or derived drinking water guideline values revealed how 2 of 65 detected compounds represent a potential risk to human health at lifelong exposure (sulfadiazine and hydrochlorothiazide), while 5 chemicals warrant additional human health impacts studies and groundwater monitoring. Although most compounds do not individually pose a significant risk to human health at current environmental levels, their potential synergistic and long-term effects remain unknown.