Efforts to evaluate water pollution using indicator microorganisms have been underway for decades, and driven by research on water purity control applications, water quality criteria are growing more and more strict. Furthermore, recent reports indicate that high concentrations of antibiotics are not absorbed, and are present in excrement from animals and humans dosed with unnecessarily high levels of antibiotics. This has emerged as very important issue from the standpoint of being an ecological and health hazard. In this study, water pollution was analyzed through physicochemical and microbiological means, and antibiotic resistance in indicator microorganisms was assessed. In physicochemical analysis, biochemical oxygen demand (BOD)$_5$ and chemical oxygen demand (COD)$_{Mn}$ evaluation showed that pollution by organisms was highest at the G1 location with a high human population, and the DP location which has many livestock-containing households. The indicator organism levels at the G1 location were: Total Coliforms (1205 colony forming units (CFU)/100 ml), Fecal Coliforms (270 CFU/100 ml), Escherichia coli (253 CFU/100 ml) and Fecal Streptococci (210 CFU/100 ml), while for the DP location levels were: Total Coliforms (1480 CFU/100 ml), Fecal Coliforms (438 CFU/100 ml), E. coli (560 CFU/100 ml), and Fecal Streptococci (348 CFU/100 ml). Levels of fecal indicator microorganisms such as Fecal Coliforms, E. coli and Fecal Streptococci were high at all locations in the fall (the period after the rainy season), and the yearly distribution was similar between these organisms. If the number of livestock-containing households was high, almost all strains of E. coli (as distinct from the other indicator organisms) showed resistance to antibiotics, with the degree of resistance varying between areas. E. coli strains from the OY area in particular, which has a high population density, showed strong resistance to AM10 and Va30. While strong antibiotic resistance was observed overall at the DP and OY locations, no resistance was observed at the EB location.