Karst rivers are special types of watercourses due to their hydrography characteristics. When rivers enter the karst, they usually disappear underground and flow through karst cavities. A self-purification of karst rivers is typically poor, because of cave conditions, e.g. absence of light and low temperature. The aim of this study is to compare surface and karst conduit flows via water quality measurement. For this purpose, two sections of the Jedovnice Brook in the Moravian Karst were chosen. First section was a part of an open channel, while the other one was a cave system Rudické propadání – Býčí skála. Measurements of water quality were provided every two weeks during 6 months at surface sampling points. Additional one-off samples were collected in the cave system. Flow rate, temperature, conductivity, dissolved oxygen concentration and pH were measured in-situ. Afterwards, content of solids, chemical oxygen demand, biochemical oxygen demand, N-NH4+, N-NO2–, N-NO3–, P-PO43– and Ptotal were determined in the laboratory. According to the results of this study, quality of water in Jedovnice brook is already poor when it enters the Moravian Karst. In the surface section, the self-purifi cation process is running well. Situation in the cave section is complicated due to underground tributaries with unknown water quality. Water leaving the cave system contains lower concentrations of the pollutants, however, overall mass flows are larger, which is evidence of pollution increase.