Caves are usually oligotrophic ecosystems, where the organic matter represents a limiting factor to the hypogeal community and sediments are often a significant energy source. With a view to identifying the energy input influencing the ecological processes occurring in caves, as well as the potential alteration sources of the natural equilibriums, geochemical features of several typologies of clastic sediments from the Pertosa-Auletta Cave (Italy) were investigated. The collected sediments, analyzed for a number of chemical (organic matter, Al, B, Ba, Ca, Cd, Co, Cr, Cu, Fe, K, Li, Mg, Mn, Mo, Na, Ni, P, Pb, S, Si, Sr, Ti, V, Zn concentrations) and mineralogical (quartz, calcite, dolomite, clay minerals) characteristics, showed a different composition. Overall, their origin is supposed to be allochthonous, related to the important fluviokarst activities interesting the cave in the past, whereas the abundance of calcitic and dolomitic compounds can be autochthonous, being the carbonate the main host rock. The highest concentrations of organic matter, together with C, Cu, Mo, N, P, Pb, S and Zn, highlighted in one sample composed mainly of bats guano, revealed an important bioavailable energy input as well as a pollutant accumulation, mainly of anthropogenic origin.