Pathogen level of surface waters has received great attention for protecting public health. In this study, total coliform, fecal coliform and Escherichia coli concentrations were monitored as the pathogen indicator organisms at six monitoring stations in the Geum River, Korea. Rainfall runoff from two agricultural-forestry watersheds was analyzed for their microbial aspect as well. Total coliform concentration of the Geum River showed high correlation with the flow rate. To estimate total coliform loading on the Geum River in probability scale, the duration curve method was applied. In addition, a standard duration curve reflecting the water quality criteria was constructed to determine water quality compliance. Under the assumption of linearity between flow rate and total coliform concentration of the Geum River, total coliform duration curve revealed that total coliform concentrations exceed the desired criteria mainly due to pollutants from diffuse sources.