Microorganisms are distributed everywhere even in extreme environments such as caves. The underground surfaces are minerals rich and the life in there is found to be related to both biotic and abiotic factors. Because the cycle of these minerals is insured by the chemolithotrophs living in there. In addition, caves are considered to be important reservoirs of bioactive compounds. However, caves are entered for different reasons. Some of the cavers are of scientific research, some of them are for recreational reasons like sports and simple cave visits. All these activities are thought to impacts the visible mat and invisible colonies of microorganisms through mechanical force or importing exogenous microorganisms. This study summarizes the different impacts which can be caused by the different human activities in caves. Finally, perspectives of the conservation of the cave microbial structure are suggested for the further uses of caves.