Climate change-induced glacier recession has sparked a dynamic transformation of glaciers in high-mountain areas worldwide, resulting in genesis, expansion, and dissipation of glacial lakes that pose a potential threat to downstream communities, underscoring the need for regular monitoring. This study incorporates the automated glacier extraction index (AGEI) to improve debris-free glacier mapping accuracy, by reducing water and shadow area categorization errors, using multi-temporal Landsat-5 TM and Landsat-8 OLI, digital elevation model (SRTM DEM), to obtain precise glacier extent. Waterbodies were delineated using thresholding techniques applied to water indices: NDWI, MNDWI, NDTI, and slope information. The study attempted to map and analyze the temporal variations of glaciers and glacier lakes in the glaciated sub-basins of Arunachal Pradesh: Dibang Basin, Mago Basin, and Subansiri Basin. Glaciers receded at a shrinkage rate of 1.08% per year (1988–2017) in Mago Basin, 1.01% per year (2013–2022) in Subansiri Basin, and 1.42% per year (1995–2021) in Dibang Basin. Glacier lakes showed an increasing trend in number and area due to glacier melt, expanding at rates of 3.31% in the Mago Basin, 0.48% in the Subansiri Basin, and 0.68% in the Dibang Basin per year. Findings suggest that global climate change is likely the primary factor driving glacier changes in these basins.