Farmer Oliver Loten has spent $50,000 on fencing to keep his sheep out of creeks and thousands more on a complex drainage system to ensure the water that pours off his fields is clean. (CBC)

An eastern Ontario farmer alleges that farmers are unfairly held to a much higher standard than cities by Ontario's Environment Ministry when it comes to allowing fecal runoff into waterways.

Oliver Loten questions why farmers can face fines and even jail time for the accidental discharge of manure into a ditch, while the City of Ottawa can regularly discharge raw sewage into waterways after a storm.

A City of Ottawa worker was fired Wednesday for failing to properly inform authorities and lying about his actions after 1.2 billion litres of sewage were discharged into the Ottawa River following a storm in July 2006, due to an Ottawa sewage system valve getting stuck open for two weeks.

The valve normally allows a small amount of raw sewage to flow into the river during storms to prevent the sewage system from backing up, but closes again after the storm. The spill was recently blamed for more than a month of bacterial contamination at the city's Petrie Island beach.

Loten, who raises sheep outside Perth, about 70 kilometres southwest of Ottawa, said he has spent $50,000 on fencing to keep the animals out of creeks and thousands more on a complex drainage system to ensure the water that pours off his fields is clean.

He questioned why the City of Ottawa's massive 2006 spill escaped investigation for so long when it likely contaminated a beach, and believes a farmer wouldn't have gotten away under similar circumstances.

"If any fish are killed, if there's any smell of manure or anything in a drainage ditch, if it affects a beach in any way, that would trigger an investigation and potentially a fine."

Ontario Ministry of the Environment John Gerretsen denied the allegations.

"We take our issues with respect to the environment very seriously and we try not to in any way, shape or form give advantage to one group over another."

The ministry has started investigating the Ottawa spill and has said charges could be laid. Gerretsen said that didn't happen sooner because the ministry only learned recently that the spill had been linked to the contamination of a beach.

Complains about double standards

Loten said the fact cities are allowed to discharge raw sewage into waterways during storms at all shows there is indeed a double standard.

If a farmer spreads sheep manure onto a field and it gets washed into a ditch by a heavy rain, there could be an automatic fine and potential jail time, Loten said.

"That same rain goes down the highway an hour and a half to Ottawa, they kick open a valve and dump a million litres of stuff into the river, and there's no issue," he said. "And that's what really has farmers upset."

City of Ottawa officials said the city has spent hundreds of millions of dollars upgrading its sewer systems to reduce the frequency and volume of raw sewage discharges after storms, but it is too expensive.

Loten countered that the Environment Ministry doesn't let farmers off the hook if they can't afford work to prevent waterway contamination.