We examined the potential for natural attenuation of ten hydrokarst systems (HKS) in three mountain units in the Carpathian Mountains. We sampled in places where water enters below ground and where water emerges back to the surface in springs and is used as drinking water by the local communities. Water samples were used to assess the degree of chemical and microbiological pollution. Although the water in the ten HKS was rather clean, a general decrease in the concentration of most chemical compounds was observed along the flow path, regardless of the number of tributaries the underground stream receives. Dilution caused by tributaries could not account for the decrease in the concentration of most compounds. The contribution of other chemical immobilization processes, such as retention of pollution in the subsurface or sorption to sediment particles was suggested, in combination with the activity of microorganisms. The bacteria diversity is complex and decreases from upstream to downstream locations due to dilution with water provided by tributaries or retention of bacteria in the subsurface by adhesion to substrates. We suggest that karst can have a significant potential for natural attenuation by retaining the pollution underground, in combination with biodegradation performed by microorganisms.