There are at least 20 fewer federal research scientists at the Canada Centre for Inland Waters in Burlington after a wave of government cutbacks over the past three years.

The most recent figures from the Professional Institute of the Public Service of Canada (PIPSC) shows that as of last month there are only 33 Environment Canada and seven research scientists from the Department of Fisheries and oceans working at the high-tech lab. As of 2010, there were 63 research scientists at the facility.

In 2000, the two organizations kept a combined 58 researchers at the site.

Scientists at the Canada Centre for Inland Waters (CCIW), a federal research centre located beneath the Burlington Skyway, study topics like pollution, toxicity and climate change in the Great Lakes area and beyond. Though the federal government touts the facility as one of its top freshwater research facilities, a large number of scientists have had their jobs "affected," meaning cut or de-funded, since 2012.

Further, many of CCIW's top scientists have been re-assigned to study the affects of Alberta's oil sands, shifting their focus away from the Great Lakes.

The centre has been a focal point for research into the cleanup of Hamilton Harbour and monitoring the progress of various remediation efforts. Hamilton's harbour cleanup watchdog group considers the cuts at CCIW a threat to the ongoing efforts to restore the bay and achieve the goal of getting it removed from the international Joint Commission list of contaminated Great Lakes sites.

Michael Arts spent 22 years working at the CCIW as an Environment Canada research scientist but quit the organization on Dec. 31, 2013, after his position was affected and then "surplussed" — an internal term he said meant his research would no longer receive direct funding.

For Arts, the message was clear: "This government doesn't support my work anymore."

Arts has since found a job at Ryerson University in Toronto, and said many of his former colleagues are also searching for new places to work. There's a "toxic" attitude at the CCIW right now, Arts said, with the general view that Ottawa is putting up barriers to all the science being done at the facility.

Arts, an expert in fish and their essential fatty acids, had several projects ongoing when he left the CCIW, including some research that was set to be published in the popular Guide to Eating Ontario Sport Fish publication. All of his research is now on hold, he said. Arts said the $750,000 worth of equipment he was using is now sitting idle, even though he's asked for permission to keep using it.

Arts said it's just another example of the government squandering the knowledge it invested in, and that the Great Lakes region may suffer as a result.

"It's very bad for the stability of science in this country."

Science cuts taking place across Canada

Spokesperson Mark Johnson said Environment Canada is currently recruiting at least one new research scientist for the CCIW, but did not comment directly on the research scientists who were affected or surplussed at the Burlington facility.

“In keeping with the Government of Canada's overall approach of fiscal restraint, Environment Canada continually seeks efficiencies in operations,” Johnson wrote in an email to CBC Hamilton.

“Environment Canada also regularly reviews and adjusts our scientific activities to ensure that available resources are allocated to be effective in achieving Environment Canada/Government of Canada objectives.”

Scientists across the country have expressed growing alarm about federal cutbacks to research programs. In the past five years the federal government has dismissed over 2,000 scientists, while hundreds of programs — some which were admired by the international scientific community — have lost their funding. Further, thousands of scientists have complained about being muzzled when it came time to discuss the results of their research.

CBC's the fifth estate highlighted many of those closures in its program Silence of the Labs, which aired last week.

Canada's Science Minister, reached by the fifth estate, said in a prepared statement last week: "Our government has made record investments in science … We are working to strengthen partnerships to get more ideas from the lab to the marketplace and increase our wealth of knowledge. Research is vibrant and flourishing right across the country."

Johanne Fillion, a communications officer with PIPSC, said it's hard even for her to figure out how many scientists have been dismissed.

"I can only give you a part of the puzzle," she said, noting the government is required to tell PIPSC when scientists' jobs have been affected, but it does not have to disclose the final outcome of that process — usually a transfer, retirement or resignation, or termination.

Fillion said 22 DFO scientists and 15 Environment Canada scientists were "affected" immediately after the 2012 federal budget. Some of those scientists were kept on staff, Fillion said, but it's not clear how many.

"At least six solid scientists left for Winnipeg," she said.

CCIW risks squandering research: scientists

Tom Muir, a retired environmental economist scientist who left the CCIW in 2004 after a 30-year career, has kept a close eye on the departures at the research facility. Muir said research scientists are crucial to maintain, because "they're the leadership of the science community."

Muir said many retiring scientists haven't been replaced and several top-earning scientists were reassigned or laid off. Muir said the CCIW has been "gutted" to the point that one former colleague told him "If I went there, I wouldn't know anybody in the place."

Arts confirmed there has been a number of cuts, but cautioned it's difficult to pinpoint the exact number as scientists are cuts are often masked by re-assignments or retirements. He said he's seen the paperwork about his own departure, which states he left Environment Canada for mandatory retirement, something he says he wants corrected.

Both Arts and Muir said the CCIW is at risk of losing some of its institutional knowledge. Further, Muir said cutting environmental science endangers the lives of those who live near the Great Lakes.

"This is the environment and people's health we're talking about," he said.

Cuts may hurt local environment groups

The Bay Area Restoration Council lists cuts to CCIW as a "threat" to its goals of monitoring the conditions and chemicals present in Hamilton Harbour, the subject of a decades-long clean-up, in its 2012 report card.

"I would be concerned with the loss of scientific capacity no matter what the reason," said BARC's Executive Director Chris McLaughlin, when told of the cuts.

McLaughlin said he doesn't advise the federal government how to spend its money, but the cuts appear at odds with the government's recent multi-million dollar investment in the Randle Reef cleanup.

He said BARC relies on the "tremendous" amount of the science generated at the CCIW, and that the research centre is this region's "greatest asset" when it comes to understanding what's happening in the area's waterways.

"There's a perception, with Google, that we know everything," said McLaughlin, stressing the importance of the scientists and their research.

"But that's far, far, far from the truth."