Commercial swine production can cause local water pollution if effluent water containing high levels of nitrogen (N), phosphorus (P), pathogen and heavy metals is discharged, but the actual status remains poorly documented. We thus selected zinc metal (Zn) as a tracer and conducted water quality observations in a rural river of Japan to reveal the significance of mid-sized swine farms on Zn pollution there. Results showed that one farm was the major contributor of Zn load in watershed, corresponding to 82% of total Zn load at a normal stage of water, which was apparently attributable to insufficient wastewater treatment at the farm. Consequently, the Zn concentration at the outlet was estimated at 37 μg L^-1, revealing a significant ecological risk at 9.1% to aquatic organisms. We then analyzed the effectiveness of improved wastewater treatment of the farm and found that it had a plausible capacity to keep Zn concentration at the outlet below the environmental quality standard level (30 μg-Zn L^-1) and the ecological risk at a safety level (<5%) as well. Based on these results, we concluded that since a swine farm could be a significant source of pollutants in rural areas, appropriate treatment of wastewater would be essential to sustain the potential pollution by Zn.