Japanese encephalitis virus (JEV) is an emerging public health and biosecurity concern in Australia, with recent human cases and detections in mosquitoes and pigs across multiple states highlights the risk to susceptible human and animal populations. While traditional surveillance relies on mosquito trapping, sentinel chicken surveillance and direct testing of samples collected from pigs, monitoring effluent provides a complementary approach for detecting infections within animal populations. This study presents the first evidence of JEV in Australian piggery effluents/environmental waters, demonstrating the feasibility of effluent and environmental water surveillance for JEV monitoring. Effluent/environmental samples from multiple piggery sites were analyzed using real-time reverse transcription (RT)-PCR, revealing the presence of JEV genetic fragments in solid and liquid effluents at three farms, with corresponding clinical cases in some herds. Viral RNA was detected more frequently in solid effluent samples, aligning with previous findings on the partitioning behaviour of mosquito-borne viruses. The detection of JEV in the borrow pit (i.e., a man-made excavation that holds water) water sample highlights potential transmission pathways via mosquito vectors. These findings demonstrate the value of effluent monitoring as an additional tool for JEV surveillance in piggery settings, supporting potential early warning systems and mitigation strategies. Integrating effluent-based monitoring with traditional surveillance approaches could improve livestock industry related disease detection, risk assessments, and response efforts for human and animal health in endemic and emerging regions. Wastewater/effluent surveillance may have important applications for the management of a wide range of emerging animal diseases.