The primary objective of the research is to understand the significance of the effects of the bedrock profile on seismic amplifications in soft soil deposits. Inclined soil-bedrock interfaces lead to simultaneous primary and secondary wave loading on soils, and a numerical study has been undertaken to assess whether ignoring them may lead to design deficiencies. The response of a site in Orleans with a deep Leda clay deposit at the center, but with a concaved bedrock profile, leading to a soft soil-deposit "valley", is evaluated using 2-D numerical analysis.The seismic response of Leda clay on a hypothetical horizontal bedrock (representing conventional practice), and two different natural bedrock basins has been studied. The National building code of Canada (NBCC 2015) design spectra compatible earthquake shaking was considered. The comparisons between the conventional practice and the response of the 2-D basin demonstrate that assessment of the cyclic loading intensity is significantly affected by the basin shape. Higher cyclic stress ratio (CSR) values are realized in the 2-D analysis due to basin geometry, and the magnitude of the CSR is dependent on the configuration of the basin. This indicates that ignoring basin geometry effects might lead to unsafe liquefaction susceptibility assessments.