Extreme heterogeneity of karst systems makes them very challenging to study. Various processes within the system affect its global response, usually measured at karst springs. Research conducted in caves provides a unique opportunity for in situ analysis of separate processes in karst underground. The aim of the present study was to research the water and air dynamics within a deep karst system. Air and water basic physical parameters across the Lukina jama–Trojama cave system (−1,431 m) were continuously monitored during a 1‐year period. Recorded hydrograph of the siphon lake at the bottom of the cave was used to interpret the characteristics of an unexplored phreatic/epiphreatic conduit network. Water origin in the siphon was determined based on temperature and electrical conductivity. Air temperature and humidity monitoring revealed a strong inflow of air of sub‐zero temperature into the upper portion of the cave during winter. Cave passage morphology was interpreted as the main determinant of air dynamics, which caused ice to accumulate extensively in the upper portions of the cave and caused the temperature on the top of the homothermic zone to be significantly below the mean outside temperature. Air dynamics also lowered the temperature of water flowing through the cave vadose zone and feeding the phreatic zone of the massif. The pronounced temperature difference between the phreatic zone and the top of the homothermic zone probably contributed to the thermal gradient observed in the cave, which is steeper than in ice‐free caves in the area. Our results enabled the development of a conceptual model that describes coupling between air and water dynamics in the cave system and its surroundings.