Erosion and deposition are two conjugate surface dynamical processes that affect differently to the soft soil site characteristics of Quaternary deposits in the Doon valley and at its northern topographic transition zone near the Main Boundary Thrust (MBT). During an impending large magnitude earthquake, what would be the seismic vulnerability and liquefaction susceptibility of the soft soil at both the regions? We quantified Seismic Vulnerability Index, effective dynamical shear strain and the expected ground deformation in the valley soft soil through H/V site characteristics using seismic ambient noise data. At the in-accessible topographic transition zone near the MBT, site effects were studied using Moderate and Light magnitude earthquakes recorded by three Broad Band Seismographs (BBS). Results show unique dual peak mean resonant frequencies (1.11 and 1.38 Hz) and amplification factors (1.69 and 1.51) at the topographic transition zone, which highlights a bimodal distribution of site effects, where the top soil formation is influenced by erosion and deposition due to topographic slope instability apart from fluvial re-working. Here, relatively compact Oldest Doon gravel is present in the foothill terraces with the re-worked fluvial deposition of the Youngest Doon gravel. However, in the valley and its terraces the soft soil formed under fluvial environ is relatively thick (10 to < 535 m) and show a distinct single peak mean amplification factor >2 and mean resonant frequency of 1.1 Hz.The spot resonant frequencies increases from 1 Hz to more than 6 Hz from the HFT region to the MBT, while the amplification factor decreases from 14 to 1. In general, the valley soft soil is susceptible for liquefaction because the estimated dynamical shear strain is 15–25 millistrains under medium (2.2 m/s2, 225 years) and long (4.6 m/s2, 2500 years) term strong motion conditions, which is much higher than the soil plasticity limit of ten millistrains that lead to liquefaction. Dynamical shear strain distribution with depth at eight boreholes in the valley indicate ∼20 m is the liquefaction potential depth, where the pore pressure induced peak shear strain exceeds the threshold shear strain of 0.01% during the passage of seismic waves. Isolated locations in the valley like that at Dharmawala (H1), where all site parameters are very high, and would be hazardously vulnerable to liquefaction. However near the MBT the liquefaction possibility of soft soil is less, but would experience ground deformation of more than 50 cm.