Abstract 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 to improve debris-free glacier mapping accuracy by reducing water and shadow area categorization errors using multi-temporal Landsat-5 Thermal Mapper, Landsat-8 Operational Land Imager, and digital elevation model (Shuttle Radar Topography Mission) to obtain precise glacier extent. Waterbodies were delineated using thresholding techniques applied to water indices: normalized difference water index, modified normalized difference water index, normalized difference turbidity index, 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.