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Climate change and rapid socioeconomic development have exacerbated the damage caused by hydrological droughts. To ensure effective drought defense and infrastructure development, it is essential to investigate variations in hydrological droughts. The primary objective of this study is to reconstruct the natural streamflow by using Soil and Water Assessment Tool (SWAT) hydrological modeling. The hydrological drought at different time scales (1, 3, 6, and 12 months) were measured using the streamflow drought index (SDI). The statistical parameters, including Nash–Sutcliffe Efficiency and the Coefficient of Determination, which yielded values of 0.84 and 0.82 during the calibration period and 0.78 and 0.76 during the validation period, respectively, showed a satisfactory SWAT model performance. Additionally, the Pettit test was used to identify a change point in streamflow within the 1991–2015 timeframe, leading to the division of the study period into two distinct phases: an undisturbed period (1991–1998) and a disturbed period (1999–2015). The SDI index‐based analysis revealed 9.39% moderate drought and 3.13% severe drought during the undisturbed period, while 11.76% moderate drought and 7.35% severe drought may happen due to the human influences that occurred in the disturbed period. These findings enhance the understanding of the hydrological drought variations in the Soan River basin for optimizing the water resources management system and effectively preventing and mitigating drought‐related damages. [ABSTRACT FROM AUTHOR]