Small-scale autonomous desalination systems (ADS) powered by renewable energy are ideal for implementation in and or semi-arid regions like the Mediterranean, especially in remote coastal or inland locations. The technology has made significant progress but wide scale implementation may face administrative barriers. This paper analyses the possible barriers imposed on ADS by the Water Framework Directive, the Drinking Water Directive, the EU Water Initiative, the European Mediterranean Partnership, and the European Neighbourhood Policy. It has been found that ADS developers have to comply with unnecessary strict regulations that apply to all drinking water supplies, while the consumers and the environment are not adequately protected from possible effects of desalination. A careful review of the relevant directives and standards has to be undertaken and adapt the documents to prepare for widespread use of ADS. On the other hand, there is widespread support for ADS within EU policy, mainly in the form of support for non-conventional water resources as well as for sustainable and rural development. The ADS community has to make use of this support and form a technology platform that will convince decision makers to improve policy and institutional framework conditions and will raise general awareness on the ADS benefits.