In tsunami studies, understanding the intricate dynamics in the swash area, characterised by the shoaling effect, remains a challenge. In this study, we employed the adaptive mesh refinement (AMR) method to model tsunami inundation and propagation in the Onagawa town physical flume experiment. Using the open-source flow solver Basilisk, we implemented the Saint-Venant (SV) equations, Serre–Green–Naghdi (SGN) equations, and a nonhydrostatic multilayer (ML) extension of the SGN equations. A hydraulic bore tsunami-like wave was used as the input boundary condition. The objective was to assess the efficiency of the AMR method with nonhydrostatic tsunami models in overcoming limitations in 2D and quasi-3D models in flume experiments, particularly with respect to improving accuracy in arrival time and run-up detection. The results indicate improved performance of the SGN and SV models in determining tsunami arrival times. The ML model demonstrated enhanced wave run-up simulations on complex built-in terrain. The refined roughness coefficient determined using the ML solver captured the arrival time well in the northern section of the Onagawa model, albeit with a 1 s delay. The AMR method offered a computationally stable solution with an 86.3% reduction in computational time compared to a constant grid. While effective, the nonhydrostatic models entail the use of a great deal of computational resources.