The ideal type of guano is found in exceptionally dry climates, as rainwater drains the guano of nitrates. Guano is harvested on various islands in the Pacific Ocean (for example, the Chincha Islands), Asian Continental especially in Indonesian ( Indonesian Guano ) and in other oceans (for example, Juan de Nova Island and Christmas Island). These islands have been home to mass seabird colonies for many centuries, and the guano has collected to a depth of many metres. In the 19th century, Peru was famous for its supply of guano.

Bat guano is usually mined in caves and this mining is associated with a corresponding loss of troglobytic biota and diminishing of biodiversity. Guano deposits support a great variety of cave-adapted invertebrate species, which rely on bat faeces as their sole nutrient input. In addition to the biological component, deep guano deposits contain local paleoclimatic records in strata that have built up over thousands of years, which are unrecoverable once disturbed.

The greatest damage caused by mining to caves with extant guano deposits is to the bat colonies themselves. Bats are highly vulnerable to regular disturbance to their roosts. Some species, such as Phyllonycteris aphylla, have low fat reserves, and will starve to death when regularly disturbed and put into a panic state during their resting period. Many species will drop pups when in panic, with subsequent death, leading to a steady reduction in population. Research in Jamaica has shown that mining for bat guano is directly related to the loss of bat species, associated invertebrates and fungi, and is the greatest threat to bat caves on the island.