Wind Cave (WICA) in the Black Hills of South Dakota, like many mostly dry caves in temperate regions is an energy-starved system. The biotic communities that reside in these systems are low in diversity and simple in structure, and sensitive to changes in external inputs of organic matter. Caves open to tourist traffic offer an opportunity to study the impacts of organic matter amendments in the form of human and rodent hair and dander, clothing lint, material from rodent activity (nesting materials and feces), and algal growth in and around artificial lighting. This study reports on the impacts of carbon amendments from humans and rodents on the bacterial and archaeal communities within the sediments of WICA from annual surveys and from a manipulative study that added lint (‘L’; cellulose plus rodent dander and rodent hair), rodent feces (‘F’), and a combination of both (‘LF’). The survey confirmed that bacterial biomass was higher in regions of the cave with the highest rates of lint (hair and natural clothing fibers) input. The manipulative study found that organic amendments in the forms of lint (L) and rodent feces (F) altered the WICA bacterial community structure in both abundance and diversity, with the combined lint and feces (LF) amendment having the most significant response. The high similarity of the LF and L communities suggests that the cave bacterial community is more carbon than nitrogen limited. The implication of cave development to management practices is immediate and practical. Even small amounts of lint and organic matter foreign to cave bacteria significantly compromise the integrity of the endemic community resulting in the replacement of undescribed species by assemblages with at best, unknown impacts to natural cave features.