Streamflow regime management is critical for preserving species in riverine and riparian habitats. Quantifying flow-ecology relationships can help to characterize the effect of flow regime change on species; however, dealing with this in ungauged catchments is challenging. By regionalizing simulation of streamflow to ungauged catchments, the Indicators of Hydrological Alterations (IHA) are calculated and used as a proxy for quantifying ecological impacts. High-resolution Regional Climate Models are used to derive the future streamflow in both gauged and ungauged catchments of the Ethiopian Rift Valley Lakes Basin (RVLB). Consequently, 32 IHAs representing the magnitude, duration, frequency, rate, and timing of streamflow events during their historical and future periods are calculated. The number of cases for future IHAs deviating from their historical range is calculated, which is called the non-attainment rate of future IHAs. A threshold value for the non-attainment rate is set to classify the impact as no-impact, low, medium, or high. The non-attainment rate for the future period indicates that, high ecological impact resulted in October, which is the local high flow month. Spatially, a shift towards a later date of the Julian date indicating the maximum flow resulted in a high ecological impact. This approach can be adapted to other regions with reliable regionalization results and suitable future climate models, which would be useful for the quantification and management of ecological impacts in ungauged regions.