To investigate the subsurface structure surrounding the Main Frontal Thrust (MFT) in central Nepal, we drilled and cored sediments to depths of 45-100 m at ten sites. Our boreholes were located along previously acquired high-resolution seismic profiles across the MFT imaging the upper 1-2 km of the subsurface, which revealed a beveled erosional surface in the hanging wall above a broad, gentle anticline, as well as growth strata in the footwall. The boreholes exhibit interlayered clays, silts, sands, and gravels, dated with optically stimulated luminescence and radiocarbon to <72.5±4.3 ka, with a transition from finer to coarser sediments at ~13.5±0.1 ka. Near the fault tip, the sediments exhibit steeper dips and deformation bands. A 25-m-thick section of silt and clay above the south end of the buried anticline is interpreted as a temporary lacustrine depocenter formed due to uplift near the fault tip. Based on the distribution of marker beds and sediment ages, we interpret a shortening rate of 3.1-12.1 mm/a on the MFT. Three major transitions between fluvio-lacustrine and coarse fluvial channel facies are inferred from the boreholes, and the timings of these transitions correlate with Indian monsoonal intensity variations linked to Earth’s precession. We infer that strengthened monsoon led to increased river discharge and advance of coarse bedload-dominant braided channels, whereas weak monsoon formed a finer-grained channel environment. These monsoonal climate variations have affected the depositional environment and river base levels in this region, influencing the formation and apparent relative uplift of nearby river terraces.