Information on Shiga toxin-producing Escherichia coli (STEC) in river water is scarce, and it is essential to understand its actual status in river water. This study investigated a method for the highly efficient recovery of STEC from river water in its active state by combining a coagulation and foam concentration and a selective medium. The method was applied to three rivers, and STEC-positive Escherichia coli (E. coli) were obtained from all rivers. Ten E. coli harboring one of the pathogenic genes (stx2, eae) were detected in the Oyodo River's upstream and midstream and the Kaeda River's midstream. Furthermore, antimicrobial agent susceptibility testing was performed on these ten strains using ten antimicrobial agents. Nine strains showed intermediate resistance to at least one antibiotic, and one was multidrug-resistant. This study's coagulation and foam concentration and selective medium detection methods can efficiently collect STEC in river water and recover it in an active state without conventional membrane filtration. Isolating and cultivating this STEC strain will provide crucial information for antimicrobial agent susceptibility testing, target gene testing, and whole-genome analysis.