Long-span structures (e.g. dams or canyon-crossing bridges) are usually located at the sites with media transition, local topography and partially filled water. However, the existing studies on the spatially variable seismic motions considering local terrains mainly focus on the single- or dual-phase media with rare consideration of the effect of media transition. Therefore, this study is motivated to present and theoretically investigate the feature of seismic motions special for a media-transition canyon with partly filled water subjected to SV-wave excitation. First, the theoretical scheme for the media-transition site needs to simultaneously cope with the issue of wave propagation in single- and dual-phase media. The key step to connecting the two different types of wavefields lies in the satisfaction of boundary conditions along with the media-transition interface. Then, to further investigate the scattering effect caused by media transition on seismic motions under different angles and frequencies, a comparative study between the models with and without the media-transition interface is performed. Results show that the feature of media transition has noticeable influences on the spatially variable seismic motions. In addition, the effect of water depth on site response is analyzed in brief. Finally, the accuracy and reliability of the whole theoretical scheme are verified. The research provides useful insights that it is reasonable to introduce the media-transition factor into the study of spatially variable seismic motions.