Integrated Hydro-Ecological Assessment for Sustainable Water Management: Anthropogenic Stress in the Main Nile Arteries—Bahr Yusuf and Ibrahimia Canals, Egypt

Global freshwater scarcity is a pressing environmental challenge, particularly in Egypt, which depends entirely on the Nile River and its tributaries. Rapid population growth, domestic wastes, agricultural runoff, and rapid industrial expansion exert highly anthropogenic stress on aquatic ecosystems, including Bahr Yusuf and Ibrahimia Canals in Upper Egypt. This study aimed to evaluate the ecological health and sustainability status of the two canals using an integrated multi-metric framework combining physicochemical variables, microbiological indicators, and community structures of zooplankton and benthic fauna. Multivariate statistical analyses (PCA, CCA), and ecological indices, including the water quality index (WQI), microbial assessment index (MAI), Rotifer-Based Index (TSIRot) and Hilsenhoff Biotic Index, were applied to determine pollution gradients. The results revealed that Bahr Yusuf suffers from higher pollution levels than the Ibrahimia Canal. Canonical correspondence analysis (CCA) showed that nutrient enrichment and elevated organic load are responsible for over 72% of the variance in zooplankton and benthic invertebrate assemblage in both water bodies. The dominance of pollution-tolerant species, Philodina roseola and B. calyciflorus of zooplankton and Limnodrilus udekemianus, Chironomidae larvae, Melanoides tuberculate and Cleopatra bulimoides of benthic taxa, further indicates a direct increase in organic loading and nutrient enrichment from agricultural and domestic sources. According to the Integrated Water Quality–Biotic Health Index (IWQ-BHI), the downstream stations of Bahr Yusuf are critical risk zones, with scores below 50.0, while the upstream stations of Ibrahimia Canal fell within the “good” category, with scores exceeding 70.0. Overall, both waterbodies are approaching a critical threshold of ecological instability and require urgent, integrated and sustainable management to restore and preserve these vital freshwater ecosystems.