Rivers face significant anthropogenic pressures due to diverse water discharges, which alter microbial community structures and may facilitate the dissemination of potentially pathogenic microorganisms and antibiotic-resistance genes (ARGs). This study used metagenomic analysis to characterize microbial and viral communities, determine antibiotic resistance profiles, and evaluate potential public health risks associated with different discharges sources. Water samples were collected from agricultural, hospital, untreated domestic wastewater, treated wastewater, and environmental inputs. Results revealed that hospital wastewater (HW) had microbial genera associated with the wastewater treatment plant; however, we were able to isolate a multidrug-resistant Klebsiella aerogenes, Enterobacter spp. and Staphylococcus spp. Untreated domestic wastewater (UW) was dominated by species such as Arcobacter cryaerophilus, Acinetobacter johnsonii, Escherichia coli, and Acinetobacter lwoffii, while treated wastewater (TW) showed the presence of Arcobacter cryaerophilus, Aeromonas caviae, Prevotella copri, Arcobacter butzleri, Acinetobacter johnsonii, Escherichia coli, and Pseudomonas stutzeri. Regarding ARGs, HW contributed significantly to ARGs diversity, particularly genes conferring resistance to critical antibiotics such as meropenem and vancomycin. TW exhibits the highest ARG diversity, including genes for broad-spectrum resistance to aminoglycosides, penicillins, and cephalosporins, suggesting cumulative contamination from multiple sources. These findings emphasize the importance of advancing efforts to tackle this challenge in wastewater treatment practices and stricter regulations to mitigate the spread of antibiotic resistance and pathogenic microorganisms in aquatic environments.