In this study, a total of 1,040 samples comprising treated Wastewater (57), Nile River water (400), and urine from suspected UTI patients (583) were collected between September 2019 and March 2020. E. coli was prevalent in Wastewater (84.2%), river water (63.3%), and 33.5% of urine samples. All extended-spectrum β-lactamase-producing E. coli (ESBLEC) isolates were fully resistant to penicillins and cephems. Multidrug resistance (MDR) was found in 70.7% of Wastewater and 87% of river isolates, with notable resistance to ampicillin/sulbactam, sulfamethoxazole-trimethoprim, and ciprofloxacin. Clinical isolates showed 62.5% MDR but remained susceptible primarily to ciprofloxacin and entirely to meropenem. Phylogenetic analysis revealed diverse chlorine-tolerant Uropathogenic E. coli strains, suggesting environmental spread.