Mountain territories are remarkably exposed to natural phenomena such as torrential floods, arising due to climate and geophysical environmental changes. Protection structures deteriorate with time due to the harsh phenomena they are subjected to since their construction. If not regularly maintained, the level of protection offered by these structures will be reduced. The methodology presented in this paper integrates physics-based and dependability models for monitoring the state evolution of protection structures and improving maintenance decision-making processes. The modeling approach proposed is based on 1) physics-based modeling for identifying the probabilistic laws of the transition times between the defined states of the structure depending on its behavior over time and 2) a decision aiding method based on Petri nets, which helps in choosing the best maintenance strategy while considering budgetary constraints. This approach is applied on a check dam located within a series of check dams in the Manival torrent in Saint-Ismier, France.