The growing global water crisis, intensified by both declining water supplies and deteriorating quality, poses acute challenges in semi-arid regions where contaminated water reuse threatens ecosystems and food security. The present study evaluates the cytotoxic and genotoxic risks of wastewater in the Tiaret region, Algeria, integrating quality of water sources to trace pollutants impacts from untreated municipal discharge to agricultural irrigation using the Allium cepa bioassay. Water samples were collected from strategic points across seasons (2023), including untreated wastewater (WW), treated wastewater (TW), Oued Nahr-Ouassel water (OW), Dahmouni dam water (DW), and irrigation water (IW) and were analyzed for organic load, nutrients, suspended solids, and ionic strength. Cytogenetic parameters were assessed via root growth inhibition, mitotic index, and chromosomal aberrations. Results revealed significant cytotoxicity and genotoxicity, with WW (high organic pollution with Biochemical Oxygen Demand, BOD5: 267.5 +/- 37.5 mg/L; Chemical Oxygen Demand, COD: 562 +/- 33.9 mg/L) exhibiting severe root growth inhibition (62-72% reduction), co-occurred with elevated mitotic indices (26.96-27.9%) and chromosomal aberrations (19.64%), due to metaphase arrest rather than productive proliferation, resolving the paradox of high mitotic indices alongside growth suppression. Genotoxicity was categorized as high (>= 15% aberrations) in WW, moderate (5-15%) in TW, OW and DW, and low (< 5%) in IW, with seasonal peaks in genotoxicity occurred in winter WW (19.6% aberrations) and summer OW (14.2%), highlighting concerns over incomplete removal of pollutants during wastewater treatment and its implication for persistent environmental and public health risks. Although partial treatment reduced genotoxicity by 23-42%, yet TW still induced metaphase arrest and micronuclei. These findings underscore the limitations of conventional treatment in mitigating pollution-driven DNA damage amplified by synergistic physicochemical stressors and provide critical insights into the implications for agricultural safety and public health. This study emphasizes the urgent needs for adaptive water management and stringent regulatory measures in semi-arid regions reliant on contaminated water for human uses and agriculture.