The cave was formed by the disappearing Reka River that gathers most of its waters on the impermeable flysch rock. Its average rate of flow before sinkholes is 8.95 m3/s, reaching up to 387 m3/s during heavy flooding. Following heavy rains, the Reka River floods in the cave, usually reaching levels up to 30 metres; the highest recorded rise in the water level was 132 metres.
The Reka River flows from the Škocjan Caves through the Karst underground and emerges to the surface in Italy some thirty-five kilometres away at the springs of the Timava River. Its flow is for the most part unknown and can only be reached in few deep shafts (up to 320 metres deep), but the siphons hinder any further exploration along the mysterious underground channels.
It is believed that prior to the Pleistocene (which lasted about two million years) the Reka River was a surface stream flowing from the flysch ground across the Karst towards the sea. Due to karstification, it was gradually disappearing underground and began to carve a gorge in the limestone bedrock, which is evidenced by river terraces. The gradual lowering of the channels through which the Reka River used to flow is also visible in the cave. The best preserved levels of the caves are the highest (oldest) ones, some of which are nowadays visited by tourists; these include the Czoering Cave, the Brihta Cave, the Window (the Mikel barn), Rimstone Pools' Hall and the Silent Cave. The Tominčeva Cave and the Schmidl Hall were formed on the lower (younger) level, at the time when the Reka River was supposedly sinking in the Sapendol collapse doline beneath the village of Gradišče. Despite having different sinks, the Reka River was essentially confined to the same channel, the Hanke's Channel, and deepened it, which resulted in the formation of such vast underground chambers.