We are interested in providing an efficient numerical scheme to represent wave propagation in time domain for configurations where a fluid domain and a solid domain are separated by a thin coating layer. Various computational challenges and bottlenecks occur in this context: incorporating fluid–solid coupling, enabling non‐conform space discretization when wavelengths greatly differ from the fluid and the solid domain, and rendering robust time discretization w.r.t. the thin layer thickness. In order to address these issues, the proposed approach combines the mortar element method with so‐called effective transmission conditions, where the effect of the coating layer is incorporated through spring—mass coefficients at the interface between the fluid and solid domain. Using discrete energy arguments, we are able to prove that the associated fully discrete scheme is stable upon a stability condition independent of the thin coating layer. Moreover, we provide an efficient time marching algorithm leading to significantly improved performances, illustrated in 2D and 3D configurations linked to ultrasonic testing experiments modeling.