A stringent environmental quality standard for zinc (Zn) has been enacted by regulators because of its toxicity to aquatic life. This study’s objective was to evaluate the variability of Zn concentrations and fluxes in the baseflow and stormflow and to estimate the contribution of Zn from point and non-point sources. By using high-resolution temporal sampling, the suspended solids (SS), iron (Fe), and Zn concentrations were measured in a small agricultural river catchment. Fe, as the natural non-point source, and Zn were evaluated using the end member mixing analysis (EMMA) to identify the source apportionment (point and non-point). The results indicate that in the baseflow, Zn mainly originated from point sources and was possibly discharged by manufacturing industries. By contrast, the non-point sources (diffuse sources) were responsible for extremely high SS, Fe, and Zn levels in the stormflow. In addition, Zn discharge during the stormflow was 93 times higher than that during the baseflow. According to the EMMA, approximately 74% of the Zn was from point sources. River management can be improved if Zn point sources are adequately treated. During a storm event, it is also important to control the particulate Zn released into the river.