Several factors were decisive for the selection of pilot regions in the IRIS project. The basic prerequisite was that the selected waters had both an ecological need for action in accordance with the requirements of the EU Water Framework Directive and a need for action in accordance with the EU Floods Directive. In order to be able to test the GE-RM planning instrument for different water body types and sizes and also for long and short river sections, rivers of different sizes were selected in the rhithral, alpine regions as well as in the potamal lowlands. The spectrum of IRIS rivers ranges from a large river such as the Danube to a small river such as the Pielach with a catchment area of only 600 km².

A further focus in selecting the pilot regions was to select rivers that cross or form provincial state borders. For these rivers, the planning process and measures must be coordinated between the affected Federal States. Within the framework of the IRIS project, such transnational planning will be tested in order to develop efficient ways for these complex coordination processes. In the case of cross-border rivers such as the Enns, separate GE-RM planning processes will be carried out by the provinces of Salzburg and Styria, which then will be coordinated. For the two border-forming rivers, Leitha and Lafnitz, the respective Federal States concerned will carry out a coordinated, joint planning process.