Extensive in-depth research is required for the implementation of natural tracer approaches to hydrogeological investigation to be feasible in mountainous regions. This review considers the application of hydrochemical and biotic parameters in mountain regions over the past few decades with particular reference to the Austrian Alps, as an example for alpine-type mountain belts. A brief introduction to Austria’s hydrogeological arrangement is given to show the significance of fractured hard-rock aquifers for hydrogeological science as well as for water supply purposes. A literature search showed that research concerning fractured hard-rock aquifers in Austria is clearly underrepresented to date, especially when taking the abundance of this aquifer type and the significance of this topic into consideration. The application of abiotic natural tracers (hydrochemical and isotope parameters) is discussed generally and by means of examples from the Austrian Alps. The potential of biotic tracers (microbiota and meiofauna) is elucidated. It is shown that the meiofauna approach to investigating fractured aquifers has not yet been applied in the reviewed region, nor worldwide. Two examples of new approaches in mountainous fractured aquifers are introduced: (1) use of CO2 partial pressure and calcite saturation of spring water to reconstruct catchments and flow dynamics (abiotic approach), and, (2) consideration of hard-rock aquifers as habitats to reconstruct aquifer conditions (biotic approach).