The present study is undertaken in the Kulsi River valley, a tributary of the Brahmaputra River that drains through the tectonically active Shillong Plateau in northeast India. Based on the fluvial geomorphic parameters and Landsat satellite images, it has been observed that the Kulsi River migrated 0.7–2 km westward in its middle course in the past 30 years. Geomorphic parameters such as longitudinal profile analysis, stream length gradient index (SL), ratio of valley floor width to valley height (Vf), steepness index (k/s) indicate that the upstream segment of the Kulsi River is tectonically more active than the downstream segment which is ascribed to the tectonic activities along the Guwahati Fault. 14C ages obtained from the submerged tree trunks of the Chandubi Lake, which is located in the central part of the Kulsi River catchment suggests inundation (high lake levels) during 160 ± 50 AD, 970 ± 50 AD, 1190 ± 80 AD and 1520 ± 30 AD, respectively. These periods broadly coincide with the late Holocene strengthened Indian Summer Monsoon (ISM), Medieval Warm Period (MWP) and the early part of the Little Ice Age (LIA). The debris which clogged the course of the river in the vicinity of the Chandubi Lake is attributed to tectonically induced increase in sediment supply during high magnitude flooding events.