More than 2,600 relict rock glaciers are known in the Austrian Alps but the knowledge of their hydraulic properties is severely limited. The relict Schöneben Rock Glacier (Niedere Tauern Range, Austria), with an extension of 0.17 km2, was investigated based on spring data (2006–2014) and seismic refraction survey. Spring-discharge hydrographs and natural and artificial tracer data suggest a heterogeneous aquifer with a layered internal structure for the relict rock glacier. The discharge behavior exhibits a fast and a delayed flow component. The spring discharge responds to recharge events within a few hours but a mean residence time of several months can also be observed. The internal structure of the rock glacier (up to several tens of meters thick) consists of: an upper blocky layer with a few meters of thickness, which lacks fine-grained sediments; a main middle layer with coarse and finer-grained sediments, allowing for fast flow; and an approximately 10-m-thick basal till layer as the main aquifer body responsible for the base flow. The base-flow component is controlled by (fine) sandy to silty sediments with low hydraulic conductivity and high storage capacity, exhibiting a difference in hydraulic conductivity to the upper layer of about three orders of magnitude. The high storage capacity of relict rock glaciers has an impact on water resources management in alpine catchments and potentially regulates the risk of natural hazards such as floods and related debris flows. Thus, the results highlight the importance of such aquifer systems in alpine catchments.