This chapter assesses the hydro-morphological condition of the studied system by developing a novel Hydro-morphological Quality Index (HQI)Hydromorphological Quality Index (HQI) following the (Rinaldi et al., in Geomorphology 180–181:96–108, 2013). This newly developed protocol uses remotely sensed data as the prime source; not chiefly implying on assessing different periods and having self-interpretative quantification. This indicator-based assessment is preceded by a three-tier segmentation of river reaches using confinement, size of the bed material and channel pattern. Thereafter a pool of 18 indicators sub-divided into three groups, i.e. continuity, planform and floodplain morphologyFloodplain morphology, are assessed for 12 reaches, 6 each for both rivers. The mean score of these measurements is termed as Hydro-morphological Quality Index (HQI) and the deviations from the least disturbed condition as DLDC. Results showed that hydro-morphological alterations are hardly visible in the confined reaches of Mahananda and Balason. However, those of Balason were slightly altered owing to a retention damRetention dam built there. Conversely, the lower reaches of Mahananda are in extremely poor hydro-morphological condition than Balason mostly due to the highly altered floodplain. Along with this, massive bank protection measures and uncontrolled sediment withdrawal also have fuelled this process. Human interventionsHuman intervention are migrating upstream which is alarming since the channel reconfiguration induced by these can engulf the upstream also.