Abstract. The impact of drought on environmental flow (EF) in 27 catchments of the Indus basin is studied from 1980–2018 using the Indicators of Hydrologic Alterations (IHA). The standardized Precipitation Evapotranspiration Index (SPEI) was systematically propagated from one catchment to another using principal component analysis (PCA). Threshold regression is used to determine the severity of drought (scenario-1) and month (scenario-2) that trigger low flows in the Indus Basin. The impact of drought on low EFs is quantified using the Range of variability analysis (RVA). The hydrological alteration factor (HAF) is calculated for each catchment in the Indus basin. The results show that most of the catchments are vulnerable to drought during the periods 1984–1986, 1991/1992, 1997 to 2003, 2007 to 2008, 2012 to 2013, and 2017 to 2018. On a higher time scale (SPEI-12), drought is more severe in Lower Indus Basin (LIB) than in the Upper Indus Basin (UIB). IHA pointed out that drought significantly impacts the distribution of environmental flow components, particularly extreme low flow (ELF) and low flow (LF). The magnitude and frequency of the ELF and LF events increase as drought severity increases. The threshold regression provided useful insights indicating that moderate drought can trigger ELF and LF at shorter time scales (SPEI-1 and SPEI-6) in the UIB and Middle Indus Basin (MIB). Conversely, severe and extreme drought triggers ELF and LF at higher time scales (SPEI-12) in LIB. The threshold regression also divided the entire study period (1980–2018) into different time zones (scenario-2), which is useful in quantifying the impact of drought on low EFs using the SPEI coefficient. Higher SPEI coefficients are observed in LIB, indicating high alterations in EF due to drought. HAF showed high alterations in EF in most of the catchments throughout the year except in August and September. The alterations are subject to several factors, including climate change, seasonality of the river flow, land use changes, topography, and anthropogenic activities. Overall, this study provided useful insights for analyzing the effects of drought on EF, especially during low flows.