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For the adequate protection of karst springs it is important to understand the functioning of karst systems in their recharge areas. Besides tracer tests with artificial tracers, tracings with natural tracers, such as temperature, are a very useful research tool, especially in complex karst systems with various types and sources of recharge. Detailed monitoring of water levels and temperatures of the Malenščica karst spring, as well as of the intermittent Cerknica Lake and Kotliči spring in its recharge area, indicated that temperature is a good tracer in winter and summer periods, especially when the Cerknica karst polje is flooded. High or low air temperatures influence the temperature of water, which sinks at the Cerknica polje and flows rapidly through karst channels toward the springs. Detailed analysis of selected events enabled calculation of the velocity of groundwater flow toward the Malenščica spring under different hydrological conditions. The estimated values are in accordance with the velocities previously defined in this area, based on several tracer tests with artifi cial tracers. From the results, it is possible to assess the transport velocities of contaminants under different hydrological conditions. This is important information for the protection of the Malenščica spring, which is captured for the public water supply.