Dispersive shock waves (DSW) are a salient feature of long water waves often observed in tidal bores and tsunami/meteotsunami contexts. Their interaction with bathymetry is poorly understood. The shoreline hazard from tsunamis and meteotsunamis critically depends on the fraction of incoming energy flux transmitted across the shallow nearshore shelf. Here, by considering nonlinear dynamics of waves over variable depth within the framework of the Boussinesq equations we show that the transmitted energy flux fraction can strongly depend on the initial amplitude of the incoming wave and the distance it travels. The phenomenon is similar to self-induced transparency in nonlinear optics: small amplitude waves are reflected by bathymetry inhomogeneity, while a larger amplitude ones pass through. The mechanism of self-induced transparency of long water waves can be explained as follows. In linear setting a bathymetry inhomogeneity, of length comparable to that of the incident wavelength, by transmitting high wavenumber components acts as a high-pass filter. The DSW evolution efficiently transfers wave energy into high wavenumber band, where reflection is negligible. By examining an idealized model of bathymetry we show that this is an order one effect and explore its dependence on parameters in the range relevant for meteotsunamis. The role of wave energy transfer into high wavenumber band owing to the growth of bound harmonics unrelated to the DSW was found to be small.