The aquatic and terrestrial ecosystems in caves are generally separate, but areas near cave streams are transitional (ecotonal) between aquatic and terrestrial cave ecosystems. Here on mud banks, the troglobitic beetles Pseudanophthalmus striatus, P. menetriesi, and Neaphaenops tellkampfi prey upon worms and other small invertebrates. As part of the community dependent upon flood-deposited organic films, the springtails Folsomia candida and Pseudosinella are preyed upon by the troglobitic harvestman (daddy longlegs) Phalangodes armata. Another major ecotone exists at cave entrances where litter from vegetation is carried in by woodrats, and also enters via gravity. Here are found the collembolans or springtails Tomocerus, Hypogastrura, Sinella, and Arrhopalites. Predators include the beetle Pseudanophthalmus, and a rhagidid mite.
The cave cricket Hadenoecus subterraneus buries its eggs in sandy passages with moderate moisture in the constant temperature zone, and the blind cave beetle Neaphaenops is especially skilled at finding those eggs. After cave crickets, this beetle has the highest density of any species in Mammoth Cave, and a small community subsists on beetle feces. The springtail Arrhopalites and the dipluran Litocampa are consumers, which are preyed upon by the mite Arctoseius, the spider Anthrobia, and the pseudoscorpion Kleptochthonius. These latter two are in turn preyed upon by Neaphaenops beetles.
In addition to eggs, cave cricket guano is also important. Crickets feed in surface habitats at night, and return to the cave to roost. Here their guano supports the millipedes Scoterpes and Antriadesmus, the springtails Hypogastrura, Arhopalites, Pseudosinella, Tomocerus, and Lepidocyrtus, plus the bristletail Litocampa, the beetles Ptomophagus hirtus and Batrisodes henroti, the snail Carychium stygius, and the mites Ceratozetes and Belba. These in turn are preyed upon by the pseudoscorpion Kleptochthonius, the beetle Pseudanophthalmus menetriesi, the larval fly Macrocera nobilis, and the spider Phanetta. As well, the spider Meta americana, and the cave salamander Eurycea lucifuga are present to prey upon crickets.
Due to low bat populations, bat guano in Mammoth Cave is today negligible as a food source for cave invertebrates, but would have been highly significant during pre-settlement times since Mammoth Cave was formerly one of the largest bat hibernacula in the world.
Woodrats and raccoons were formerly abundant in Mammoth Cave, and though today reduced, their feces support specialized communities. Latrines of the Eastern Woodrat Neotoma floridana sustain larva of the fly Psychoda and fungus gnat Bradysia, and the beetle Ptomaphagus hirtus, which are preyed upon by the rove beetle Quedius. Raccoon feces support a similar community with the exception that cave crickets may preempt fly larvae, most notably Spelobia, and Amoebelaria.