Karst caves are important tourism and natural heritage destinations. Within dry cave passages otherwise notable for their rich flowstone decoration, areas with a characteristic black color can sometimes be observed on cave walls and floors and on speleothems. To determine the origin of these black deposits, mineralogical and chemical analyses were carried out in two caves (Postojna Cave and Črna Jama (Kočevje), Slovenia). Qualitative chemical composition was obtained by scanning electron microscopy in conjunction with energy dispersive X-ray spectrometry (SEM/EDS). Organic matter in black deposits was confirmed by the Walkley–Black (wet burning) and loss-on-ignition (LOI, dry burning) methods. Results showed that black deposits from the caves studied could be attributed to natural and anthropogenic causes. Natural causes are related to Mn–Fe oxide precipitation and are probably dependent on microorganism activity. Anthropogenic sources are related to historic (or/and prehistoric) human activities such as cave visitors using torches and fires, events outside the caves such as forest and settlement fires, and recent air pollution. Black deposits show the effect of long-term environmental impact on karst caves and could be included in guided tours of show caves along with a scientific explanation of their causes and origin.