The upper Ganga basin (UGB) constituting Bhagirathi and Alakananda basins has been considered as a single hydrological unit so far with comparable climate forcing. Here, we show three distinct “topoclimatic zones” of this basin having characteristically different temperature, precipitation, and orographic processes. The orographic discontinuity forced by a mountain ridge with an average elevation of 5,200 m a.s.l. is instrumental in the development of these topoclimatic zones. The northern region of the basin is identified as high elevation and high temperature zone (HE‐HT) with monsoon moisture deficit. This monsoon deficit region is characterized by higher land surface temperature lapse rate (LSTLR) during July and August (JA) derived from MODIS‐LST (11.00°C/km) as compared to much lower LSTLR of monsoon topoclimatic zone (5.78°C/km). The nival‐glacier regimes of the monsoon dominant and monsoon deficit regions constituted the third topoclimatic zone characterized by high elevation‐low temperature zone (HE‐LT). This zone has comparatively lower temperature lapse rate (5.26°C/km) than the immediately lower elevations. The coldest points identified in the basin are mostly placed in monsoon deficit regions with higher LSTLR. The 10–12°C isotherm in the monsoon deficit zone runs at 5,300 m a.s.l. as compared to 3,200 m a.s.l. in monsoon dominant zone. It is proposed that 80% of glacier area in the UGB is in the monsoon deficit zone that is regulated by the northern region orographic processes rather than southern slopes. Glacier change in the southern and northern zones show significant difference during the period of 1994–2016/2017, with significantly higher glacier area loss in the HE‐HT zone. The study highlights the importance of these topoclimatic considerations while evaluating the climate and hydrology of UGB.