This paper studies the effects of spatially varying ground motions on the responses of a bridge frame located on a canyon site. Compared to the spatial ground motions on a uniform flat site, which is the usual assumptions in the analysis of spatial ground motion variation effects on structures, the spatial ground motions at different locations on surface of a canyon site have different intensities owing to local site amplifications, besides the loss of coherency and phase difference. In the proposed approach, the spatial ground motions are modelled in two steps. Firstly, the base rock motions are assumed to have the same intensity and are modelled with a filtered Tajimi-Kanai power spectral density function and an empirical spatial ground motion coherency loss function. Then, power spectral density function of ground motion on surface of the canyon site is derived by considering the site amplification effect based on the one dimensional seismic wave propagation theory. Dynamic, quasi-static and total responses of the model structure to various cases of spatially varying ground motions are estimated. For comparison, responses to uniform ground motion, to spatial ground motions without considering local site effects, to spatial ground motions without considering coherency loss or phase shift are also calculated. Discussions on the ground motion spatial variation and local soil site amplification effects on structural responses are made. In particular, the effects of neglecting the site amplifications in the analysis as adopted in most studies of spatial ground motion effect on structural responses are highlighted.