A study was conducted to investigate the presence of E. coli and antibiotic-resistant E. coli at 15 sites, including 8 tidal rivers flowing into Urado Bay in Kochi Prefecture and a beach outside the bay. Water samples were collected during both fair weather and rainy conditions. The results showed an increase in bacterial counts during rainfall compared to fair weather. Based on the relationship among rainfall patterns, bacterial counts, and the salinity of water samples, it is suggested that increased microbial loads from upstream river areas and the bay's seawater could be potential sources of contamination during rainfall. A trend was also observed where greater total rainfall was associated with a larger increase in bacterial counts in the rivers. Additionally, at locations where seawater from Urado Bay flows back upstream, a detailed investigation of bacterial count variations was conducted through continuous water sampling during both fair weather and rainfall. The findings confirmed that during fair weather, the backflow of seawater from Urado Bay led to a reduction in the number of E. coli and antibiotic-resistant E. coli in the rivers due to dilution and other effects. During rainfall, both seawater from Urado Bay and runoff from upstream river areas could be a sources of contamination.