Seismic site effects are predicted adopting ground response analysis for the fluvio-lacustrine deposits of Kathmandu Valley using available geotechnical data. Equivalent linearization of nonlinear soil model has been analyzed for the study area with the geotechnical database up to the engineering bedrock level. The amplification ratio has been estimated to be varying from 1.9 to 7.8. As the peak spectral acceleration and predominant period largely contribute in the damage of structures, higher values of these parameters are consistent with the damage during 1934 Bihar–Nepal earthquake. The peak spectral acceleration for Kathmandu Valley has been estimated in a close range of 1.2725–1.2826 g. Meanwhile, the predominant period of valley soil varies from 0.27 to 0.61 s, representing the possible resonance, as 3–6 stories structures are the majority constructions in the study area. It has been contemplated that the upper 30 m of Kathmandu Valley soil would undergo large amplification with higher spectral acceleration and the predominant period shows the higher possibility of resonance with the construction trend of the buildings.