Hospital effluents represent a significant source of chemical, microbiological, and pharmaceutical contaminants that can compromise water quality and promote the spread of antibiotic-resistant bacteria. This study aimed to assess the physicochemical and microbiological quality of hospital effluents (R1) from the Ahmed Ben Bella hospital, treated wastewater (R2) from the treatment plant outlet and downstream of the discharges (R3) from Oued Baghai River at (Khenchela, Algeria) to evaluate treatment efficiency and associated environmental risks. Physicochemical parameters were determined using standardized methods, while microbiological analyses included the enumeration of total coliforms, fecal coliforms, and fecal enterococci, bacterial identification using the API 20E system, and antibiotic susceptibility testing via the disk diffusion method. Results demonstrated that hospital effluents (R1) exhibited a high organic load of chemical oxygen demand (COD): 132.52 mg/L, five-day biochemical oxygen demand (BOD5): 52.20 mg/L), elevated concentrations of ammonium and phosphates and bacterial contamination exceeding recommended standards. Microbiological analyses revealed the persistence of coliforms and fecal enterococci throughout the treatment process (R2). Twelve species of Enterobacteriaceae were identified, with predominance of Escherichia coli across all sampling sits (R1, R2, and R3). Antibiotic resistance profiles showed a high prevalence of multidrug-resistant strains in the hospital effluents (R1), while levels decrease progressively following treatment, the strains were not completely eliminated. Thus, the conventional treatments used by the wastewater treatment plant to eliminate microbiological contaminants and multidrug-resistant bacteria were limited. Integration of advanced treatment processes and enhanced water quality monitoring prior to any agricultural reuse are recommended to protect aquatic ecosystems and public health.