Rishi Khola, a sub-watershed of Teesta river, traverses along the Main Central Thrust (MCT) with a multitude of litho units and structural entities. This study examines the impact of tectonic and lithologic controls in configuring the catchment characteristics of Rishi Khola, Sikkim, India. Corrected SRTM 30 m DEM and Landsat 8 satellite image have been used for extracting the river network, preparing the sub-catchments, the longitudinal profile and thereby calculating the morphotectonic indices. An aggregated tectonic index (ATI) has been prepared to map the intensity of tectonic perturbations in the fluvial environment using the entropy weightage method (EWM) and Weighted Linear Combination (WLC). The undulating nature of the longitudinal profile with prominent knick points confirms the presence of tectonic disturbances and lithological variations. From all the computed morphotectonic indices and the ATI, it has been evident that the region has experienced surface deformations. When viewed at the entire catchment, the morphotectonic indices suggest ample responses to the tectonic perturbations due to the dominance of lithology-controlled hill slope processes and fluvial erosion. The spatiality of the tectonic sensitiveness is rather concentrated into certain pockets of differential stress field formed due to fault thrusting of the Himalayas. The study chiefly focuses on the peculiarity of the watershed which displays a complex response of tectonic and rock structure; wherein the proposed methodology has been successful in excavating such complex responses around the Himalayan thrusts.