Zinc (Zn) and copper (Cu) are toxic to aquatic organisms at very low concentrations that do not affect humans. We measured the daily output of Zn and Cu in wastewater from livestock farms to aquatic environments because waste from animal husbandry operations contains high levels of Zn and Cu. At most pig farms in Japan, a mixture of urine, some faeces, and service water is treated in onsite wastewater treatment facilities and discharged into a water body. Some dairy farms also have wastewater treatment facilities. We surveyed 21 pig farms and six dairy farms. The unit (i.e., per head) output load from piggery wastewater treatment facilities ranged from 0.13 to 17.8 mg/head/d for Zn and from 0.15 to 9.4 mg/head/d for Cu. Over 70% of pig farms had unit output loads of Zn and Cu below 6 and 2 mg/head/d, respectively. For dairy farms, the unit output load from wastewater treatment facilities was estimated at 1.8-3.6 mg/head/d for Zn and 0.6 mg/head/d for Cu. The unit output load for Zn from piggery wastewater treatment facilities was similar to that from treatment facilities for human waste. However, pig farms generally raise several thousand to tens of thousands of pigs; pig farms are therefore presumed to be a significant point source of Zn in rural areas.