In the catchment area of the Unica River two combined tracer tests with fluorescent dyes have been performed aiming to characterize the properties of groundwater flow and transport of contaminants through the vadose zone and well developed system of karst channels in the epiphreatic and phreatic zone in different hydrologic conditions. Tracers were injected directly into the ponors and to the oil collector outlet on the karst surface. Prior to tracing monitoring network has been set up, including precipitation, physical and chemical parameters of the springs and cave streams. Field fluorimeters were used to detect tracers in the underground river and conventional sampling techniques and laboratory analyses were used at the springs. Some of the results were quantitatively evaluated by QTRACER2 Program. During the first tracer test, when injection was followed by rain event, flow through the well conductive cave system was characterized by apparent dominant flow velocities of 88–640 m/h. Breakthrough curves were continuous, uniform and single peaked, and almost complete recoveries were observed. During the second tracer test, when water level was in constant recession, the transport velocities through the well developed karst conduits were significantly slower (apparent maximal flow velocities being 2–4 times lower). Results also show lower dispersivity during the second tracer test, which corresponds to lower flow velocities. The tracer injected at the karst surface arrived with the expected delay (vdom around 9 m/h) and showed irregular and elongated breakthrough curves with secondary peaks. In this paper only tracer test results are presented, which are a part of a comprehensive study of groundwater flow through the complex karst aquifers aiming at improving karst water resources understanding, protection and management. The presented assessment will beyond be utilized for further detailed analysis, studies and modelling.