Finite element method (FEM) modeling is devoted to flexible structures, such as fishing gear and fish-farming cages. Floating barriers named booms are moored during oil spill emergencies in the vicinity of a shore respecting geomorphology and environmental conditions to ensure containment or deviation of hydrocarbon slicks. The state of the art concerning oil booms focuses mainly on their hydrodynamic performances. Their behaviors are investigated under current and waves showing the Kelvin–Helmholtz instability of the oil–water interface. This chapter briefly describes the MOHID water modeling system and its main applications. The use of the operational model MOHID allows to reduce the impact of marine pollution. Its efficiency is guaranteed by three intrinsic properties, versatility, interoperability and operationality.