To ensure the safety of Kimchi, the safety of Napa cabbage is the most important. Contaminated irrigation water can be a major cause of pathogens during growth of Napa cabbage. The purpose of this study was to investigate the microbial quality of irrigation water used in the cultivation of Napa cabbage. A total of 111 samples including surface water (n = 75) and groundwater (n = 36) collected from four different regions in Korea where Napa cabbage is intensively cultivated were analyzed for a fecal indicator (Escherichia coli) Moreover, 164 E. coli isolates from irrigation water were investigated for pathogenic characteristics including antibiotic resistance, pathogenic genes, serotype, and toxicity using Caenorhabditis elegans. E. coli was detected in 96% of surface water samples and 25% of groundwater samples. The level of E. coli in surface water (0.2-3.2 log MPN/100 mL) was higher than that in groundwater (0-2.0 log MPN/100 mL). When the 164 E. coli isolates were investigated concerning antibiotic resistance, resistance rates were 11.0%, 2.4%, 3.0%, 1.8%, 2.4%, 4.3%, and 3.0% for ampicillin, ampicillin/sulbactam, cefazolin, cefoxitin, gentamicin, levofloxacin, and trimethoprim/sulfamethoxazole, respectively. In addition, 10 (6.1%) of the isolates were positive for the eaeA gene, indicative of enteropathogenic E. coli. Eight of these 10 isolates were obtained from the surface water of the mountainous region II and were toxic to C. elegans. The results indicate the need to manage the microbial risk of irrigation water to enhance the safety of cultivated Napa cabbage.