The behaviour of aquifers with karst porosity is dependent on hydrological conditions. This is due to the peculiar characteristics of the groundwater flow and dynamics of hydrological processes in karst. As a result, karst aquifers are especially vulnerable to the effects of environmental change. We assessed the long-term climatological and hydrological trends and the short-term effects of increasingly frequent extreme hydrological events (droughts) for the Mediterranean karst spring Rižana in SW Slovenia. The findings predict higher mean annual air temperatures of 0.34°C decade⁻¹, lower annual precipitation of c. 60 mm decade⁻¹ and higher annual actual evapotranspiration (especially during spring and summer) of 32–49 mm decade⁻¹. As a consequence, we can expect a decrease in the mean annual discharge of the spring of c. 480 l s⁻¹ decade⁻¹ with prolonged dry summer periods. Detailed monitoring of the physical, chemical and microbiological parameters showed that the flood pulses caused by precipitation events after a long dry period cause a significant deterioration in water quality. In such situations, contaminants stored in the unsaturated zone are flushed out and counts of coliform bacteria can reach >1400 cfu (100 ml)⁻¹, with total Al and Fe concentrations up to 206 and 474 μg l⁻¹, respectively. These results suggest that there should be urgent adherence to water quality standards to protect karst water sources in view of the anticipated climatological stresses. Management strategies should promote monitoring and the rational use of karst water supplies.