The installation of geoenergy systems on designated groundwater areas in Finland is regulated by the Water Act and the Environmental Protection Act through the water permit procedure. We analysed permit documents to trace the temporal development of application numbers and permit policies, and the scientific and legal principles guiding the permit procedure. We discovered that, since geoenergy issues were not considered when enacting the legislation, it provides little support for geoenergy permit decisions. Consequently, the role of soft law documents is emphasised. Further technical and scientific instructions are also needed to support geologically sound reasoning in permit decisions. On the other hand, deficiencies in many permit applications highlight the need for more professional preparation of applications and system designs.