We examined water quality indicators (pH, temperature, turbidity, total phosphorus, and fecal coliform density) and bacterial antibiotic resistance (prevalence, conjugative transfer, and genetic linkage of resistance elements) at locations impacted by confined animal feeding operations (CAFOs) and compared them to nearby reference sites. Sites located upstream and downstream of two wastewater treatment facilities were also compared. Sites near CAFO farms had poor water quality (elevated total phosphorus and turbidity), while water quality remained relatively good downstream of wastewater treatment plants. High proportions of antibiotic-resistant bacteria were observed at all study sites, and frequent conjugative transfer of resistance was observed in laboratory assays. Out of a total of 830 environmental bacterial isolates, 77.1% were resistant to only ampicillin, while 21.2% were resistant to combinations of antibiotics including ampicillin (A), kanamycin (K), chlorotetracycline (C), oxytetracycline (O), and streptomycin (S). Multi-drug-resistant bacteria were significantly more common at sites impacted by CAFO farms. In conjugation assays, 83.3% of the environmental isolates transferred one or more antibiotic resistance genes to a laboratory strain of Salmonella typhimurium. A subset of multi-drugresistant (A, C, and O) isolates was screened for specific tetracycline resistance genes and class I and II integrons. None of the screened isolates (n=22) were positive for integrons, while 13 isolates contained resistance genes for tet (B) and tet (C). Our results indicate that CAFO farms not only impair traditional measures of water quality but may also increase the prevalence of multi-drug-resistant bacteria in natural waters.