Many activities have the potential to affect subterranean caves and their inhabitants. Inadequate sewage treatment rapidly leads to pollution of the ground water, directly threatening aquatic fauna, but ultimately affecting all cave fauna. Deforestation can affect water flow patterns so that in general there will be less buffering and flooding will increase in frequency. Alteration of cave entrances, such as removal of vegetation or physical changes in rock structure, will change airflow patterns, oxygen concentrations, temperature, humidity, and light regimes. Cave species tend to be very sensitive to the smallest microenvironmental changes, with a result that they are unable to adapt to changes and go extinct or, if possible, abandon the cave.

Some cave systems have considerable capacity to sustain visitation, such as those with large rivers passing through underground caverns. Others have less capacity. High-energy caves with guano deposits can be exploited only if measures are taken to ensure the survival of the guano fauna and not disturb the bat colonies. Low-energy caves with numerous pockets of stagnant air are extremely vulnerable and the first party of tourists, if they are not subdued by the heat, dampness, and the bad air, may do considerable damage.

Specific risks that need to be understood in the exploitation of cave resources or development of caves for tourism include:

• Soil-dwelling cave inhabitants may be trampled to extinction or compaction of soil will reduce aeration and abilities of organisms to penetrate the substrate
• Compaction of sediments may have synergistic effects in that more water is channeled through the cave, sediment may be eroded, infilling of cave pools occurs, cave biota may be smothered by poor aeration
• Disturbance of water pools increase turbidity and particle suspension
• Bats are sensitive to lights and noise. Species that pollinate commercially important plants or are important pest control agents may abandon a disturbed cave and leave the area in the absence of suitable alternative sites, which may cause significant financial and ecological loss
• Quasi-permanent lighting will stimulate the growth of algae, moss, ferns and other terrestrial fauna
• Specimen collection: cave invertebrates show high levels of endemism and small populations within a cave system, which renders them vulnerable to extinction.

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