Managed aquifer recharge (MAR) can be affected by many risks. Those risks are related to different technical and non-technical aspects of recharge, like water availability, water quality, legislation, social issues, etc. Many other works have acknowledged risks of this nature theoretically; however, their quantification and definition has not been developed. In this study, the risk definition and quantification has been performed by means of “fault trees” and probabilistic risk assessment (PRA). We defined a fault tree with 65 basic events applicable to the operation phase. After that, we have applied this methodology to six different managed aquifer recharge sites located in the Mediterranean Basin (Portugal, Spain, Italy, Malta, and Israel). The probabilities of the basic events were defined by expert criteria, based on the knowledge of the different managers of the facilities. From that, we conclude that in all sites, the perception of the expert criteria of the non-technical aspects were as much or even more important than the technical aspects. Regarding the risk results, we observe that the total risk in three of the six sites was equal to or above 0.90. That would mean that the MAR facilities have a risk of failure equal to or higher than 90 % in the period of 2–6 years. The other three sites presented lower risks (75, 29, and 18 % for Malta, Menashe, and Serchio, respectively).