The rapidly increasing renewable energy installations are often controlled through permit schemes, and good permit practices need to be developed for energy policy planning purposes. In Finland ground heat exchangers (GHEs) for geoenergy systems commonly need a permit from the municipal building control. We examine this municipal permit scheme, its functionality in groundwater protection and compatibility with the principles of good governance. Our data consists of permit and notification documents, interviews of building control officials and municipal regulations and instructions from nine municipalities in Southwest Finland. Similar studies based on empirical data have not been conducted earlier on geoenergy permit schemes. Despite common legislation there were many differences between municipalities in the application-stage permit practices, municipal regulations, supervision and quality control of GHEs. Well-functioning permit practices safeguard both the public and the neighbors’ interests, promote groundwater protection and support the client with quality control.