The ultimate objective of the Water Framework Directive 2000/60/EC is protection of waters and water environment for the future generations. Achieving good condition of all parts of waters is done by setting up and implementing the necessary actions within the integrated programmes in the member states. The selected the so-called uniform parts of waters (both surface and underground) should be protected to be left in good quantity and quality condition for the future generations. Investments in renewable sources of energy are recognised, in the light of the European Parliament and Council Directive 2009/28/EC of 23 April 2009 on the promotion of the use of energy from renewable sources as promoted sources of energy due to the care for the environment. Thus, the benefits from execution of such investments are highly valued in both regional and global scale, especially in reference to climatic changes and continued pollution of the environment. National experience in execution of small hydropower plants prove, however, high degree of ambiguity and pose many controversies. Both positive and negative effect of execution of small hydropower plants highly depend on the specific location and on the current condition of the environment. The article presents the legal regulations in force and the possible interactions of the project limited to the analysis of the effect on protection of uniform parts of groundwater.