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Spatio-temporal analysis of waterbodies in terms of detection of morphological change could serve as a guiding tool to restore the lentic ecosystem. This research analysed the loss of lake extent within 50 years (1969–2019) through natural, anthropogenic reasons, as well as a lack of attention to protecting lakes in the Tarai region. In 1969, 75 lakes were found, but now only 46 lakes are alive. Among the 75 lakes, seventeen transformed into large ponds after reduction in extent, and twelve lakes either appeared as waterlogging zones during the rainy season or were permanently extinct and used as agricultural fields’ built-up activities. The spatial vulnerability index (SVI) measured the level of deterioration and urgency of lake restoration. 8 lakes were determined to be highly vulnerable (below 29.26%) and lost about 311.20 hectares of potential area of lake beds due to gradual increasing shallowness …