The flow regimes of most rivers around the world have been impacted by human activities. This has resulted in the loss or disruption of natural hydrological variability and, in turn, in extensive ecological damage. River regime alterations have the potential to cause the collapse of the local ecosystem by impairing existing habitats and causing widespread and/or cascading extinctions. In this study, we employ the Indicators of Hydrologic Alteration (IHA) metrics in combination with change point analysis to quantitatively analyze changes in streamflow across two river basins in South India, namely, Cauvery and Krishna. The findings demonstrate that the change points that have been identified in the river basins do, in fact, represent times when the hydrological indices—which represent the different aspects of the flow regime—underwent notable changes. The IHA analysis suggests that in the Cauvery Basin, there has been a shift toward an increasingly controlled flow regime with diminished monsoon flows at all stations surveyed. Streamflow has also decreased throughout the year (more than 50%) at the majority of the stations. The Krishna basin, on the other hand, has experienced increased flows and hence improved surface water availability, but with potential flood risks. The study emphasizes the urgent need for adaptive water management strategies that address the human-induced causes of altered river flows in the region.