Aquaculture products, such as clams, scallops, and oysters, are major vectors of fecal-derived pathogens. Male-specific and somatic coliphages are strongly correlated with human noroviruses, the major enteric viruses worldwide. Geographic information system with local land-use patterns can also provide valuable information for tracking sources of fecal-derived pathogens. We examined distributions of four fecal indicator microorganisms, i.e., male-specific and somatic coliphage, total coliform, and Escherichia coli (E. coli) in three river and seawater sampling sites located on the coast of Gomso Bay in the Republic of Korea during the sampling period (from March 2015 to January 2016). Geospatial analyses of fecal indicators and correlation between environmental parameters and fecal indicators or among fecal indicators were also performed. Overall, river water samples showed highest concentrations of both types of coliphage in summer (July 2015). High concentrations of both total coliform and E. coli were detected in river water during the period from July to September 2015. High concentrations of all fecal indicators were found at site GL02, located in the innermost part of Gomso Bay, which has high-density agriculture and residential areas. Environmental factors related to precipitation-cumulative precipitation on and from 3 days before the sampling day (Prep-0 and Prep-3, respectively)-and salinity were strongly correlated with concentrations of all fecal indicators. The present results suggest that investigations of multiple fecal indicators with a systemic geospatial information are necessary for precisely tracking fecal contaminations of aquaculture products.