Safety of dams and other hydraulic structures is a complex procedure that must consider the individual characteristics of each structure and provide an insight in the structural health at every stage of the structure’s life cycle. Failures of structures permanently or temporarily retaining water may cause large economic damage, environmental disasters, and loss of lives. An engineering design should, therefore, guarantee maximum security of such structures or maximize their reliability not only in ordinary operating conditions but also under extreme hydrological load. By performing structural heath monitoring (SHM), the safety can be optimized, including the performance and life expectancy of a structure by adopting an appropriate methodology to observe the identified failure modes for a selected dam type. To adopt SHM to hydraulic structures it is important to broaden the knowledge and understanding of the ageing processes on hydraulic structures, which can be achieved by laboratory testing and application and development of novel monitoring techniques, e.g., vibration monitoring. In Slovenia, we are increasingly faced with the problem of ageing of dam structures. At the same time, we are also faced with changes in the environment, especially with the variability in time-dependent loads and with new patterns of operation on dams used for hydropower, with several starts and stops of turbines happening on a daily basis. These changes can lead to a decrease in structural and operational safety of dams. In this paper we propose a methodology where the dynamic response of concrete dams is continuously monitored in few locations on the dam using accelerometers, while all significant structural members are measured in discrete time intervals using portable vibrometers. We focused on run-of-the-river dams, which are a common dam type in Slovenia. The pilot case for the system is lower Sava River with a cascade of 5 dams used for hydropower.