WODONGA saleyards operator, Regional Infrastructure, will pay a $6107 fine from the EPA after effluent was discharged into Middle Creek.

EPA North East manager Clare Kiely said officers found effluent had been discharged into local waterways in August last year due to a poorly maintained, an outdated effluent treatment system and high rainfall.

"EPA officers tracked the discharge to the effluent management system and saw that it was leaving the premises and flowing into a local waterway, Middle Creek,"  Ms Kiely said.

"Officers took samples of the discharge and inspected the saleyards, concluding that the high recent rainfall and poorly prepared irrigation and effluent management system had been overloaded with a combination of untreated and partially treated effluent and stormwater."

Wodonga saleyards operations manager James Thompson told Weekly Times Now the incident occurred after "two or three days of heavy rain and trickled over a holding bank".

He said last year's increased rainfall put pressure on the system and the company had worked with the EPA and updated its water treatment and irrigation system.

Mr Thompson said the company would pay the fine.