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In this paper, we investigate long-crested wave evolution over a cross-section of non-monotone bathymetry. The bathymetry is from an area with an isolated shallow seamount on the south coast of Java Indonesia near Glagah port. We will investigate waves with a significant wave height (H s) of 2 m and more energetic waves of 4 m over a cross-section through the top of the seamount that is only 2 m under sea level and located 8 km from the coast. The wave simulations over a 12 km long cross-section to the beach are used to determine the numerical and physical aspects of the wave transformation over bathymetry, including breaking properties, the effect of bottom friction, and differences between second and third order simulations. This study used HAWASSI software for irrotational fluid dynamics with a Fourier spectral method implementation. Crossing the top of the seamount leads to a transformation from the wind waves into a downward running flow described by very long infragravity (IG) waves that persist until the nearshore area with the run-up area of the coast. [ABSTRACT FROM AUTHOR]