Improving water quality is a critical issue worldwide. However, the general parameters (i.e., temperature, pH, turbidity, total solids, fecal coliform, dissolved oxygen, biochemical oxygen demand, phosphates, and nitrates) used in water quality index estimations are unable to identify pollution from industrial wastewater. This study investigated pollution sources at a river pollution hotspot by using the positive matrix factorization (PMF) model. A two-phase sampling collection along a highly polluted river in northern Taiwan was designed. The sampling spots were distributed along the river in Phase I to monitor the spatial variation of river pollutants. A pollution hotspot was determined based on two indices, namely the summed concentrations of elements and a metal index (MI). In Phase II, the river water samples were collected from the hotspot twice daily over 30 consecutive days to monitor the temporal variation of river pollutants. Source profiles of metal elements were obtained during the monitoring period. The Phase II samples were then factorized using the PMF model. Factor profiles retrieved from the PMF model were further assigned to industrial categories through Pearson correlation coefficients and hierarchical classification. The results indicated that the main pollution source was bare printed circuit boards (BPCB), which contributed up to 92% of the copper in the pollution hotspot. In terms of MI apportionment of 11 metals related to health effects, BPCB contributed 91% of the MI in high pollution events. Overall, the MI apportionment provides linkages between pollution level and human health. This is an evidence for policymakers that the regulation of the effluents of BPCB is an effective means to controlling copper concentrations and thus improving water quality in the study area.