The biggest challenge in the enormous task of cleaning up Hamilton Harbour is also one that has troubled environmentalists for decades: excessive phosphorus.

Phosphorus, a nutrient that increases productivity in water, causes algae to grow excessively and disrupts the food chain and the ecosystem, explained John Hall, coordinator of Hamilton Harbour Remedial Action Plan.

We've come a long way in making improvements to the harbour, but we still have substantial work ahead of us. - RAP coordinator John Hall

Known as RAP, the plan was developed by more than 40 stakeholder groups in the 1980s to clean up the harbour.

“We've had far too much phosphorus, so the system is way overproductive,” Hall said. “We really want to push the productivity down so it's a more balanced system.”

Hall is one of the participants of the annual Conference on Great Lakes Research taking place at McMaster University this week.

Now in its 57th year, the conference, hosted by the International Association for Great Lakes Research, offers 50 sessions and is expected to bring more than 600 scientists and researchers to the McMaster campus.

Hamilton Harbour was put under the spotlight during a full-day session on Tuesday, during which a dozen researchers presented their studies on topics ranging from the influence of viruses and zooplankton production to the gene expression of rainbow trout and the population trends of colonial waterbirds.

Even though phosphorus levels have been dropping steadily, the current level in the harbour — 40 micrograms per litre — is twice the accepted level, Hall said.

The harbour has been battling excessive phosphorus level for decades. The reading when RAP first began its work in the 1990s was 80 micrograms per litre, down from a staggering 160 micrograms per litre 15 years ago.

Phosphorous remains a major water quality problem in the restoration of Hamilton Harbour. (CBC)

Phosphorus is commonly found in fertilizer, detergent and animal feed. It enters the water system through wastewater, as well as stormwater that washes down farm fields and city streets, picking up contaminants containing phosphorus along the way.

Phosphorus levels remain an issue in the open waters of three of the four Canadian Great Lakes, according to Environment Canada.

RAP has introduced two solutions to lower the phosphorus level for a clearer harbour and a more diverse ecosystem: upgrading the wastewater treatment plants and improving stormwater management.

Wastewater accounts for half of phosphorus flowing into the harbour, according to Hall. With a $480 million investment to upgrade the harbour's two wastewater treatment plants — the Woodward plant and the Skyway plant — the level of phosphorus can be lowered substantially.

RAP is also working with municipalities and conservation authorities to better manage watersheds during storms, the second biggest contributor of phosphorus.

Water quality – indicated by the level of phosphorus — is not only the biggest challenge, it is also the weak link in the remediation effort, Hall said. Once the water quality is improved, fish and wildlife will also benefit.

“In an ecosystem approach where everything is connected to everything else, you move at the pace where the limitation is and the limitation is water quality,” Hall said.

Centuries-old problem

The problem brewing at the harbour has been decades, if not centuries, in the making.

Starting from 1800s, chemical, industrial and thermal pollution began degrading the harbour and waste boomed in the early 1900s, according to an Environment Canada study presented at the conference on Tuesday.

By 1950, the harbour had become unfit for recreational use and all beaches were shut down.

The ambitious goal to clean up the harbour is now “half way there,” Hall said. RAP has set 2020 as the deadline to restore what was once considered one of the Great Lakes' most polluted water bodies.

“We've come a long way in making improvements to the harbour, but we still have substantial work ahead of us,” he said.

One of the milestones of the remediation effort is the $139.9 million investment to clean up Randle Reef, the harbour's most toxic hot spot.

The project, announced in September 2013, is jointly funded by the federal and provincial government, the City of Hamilton, the Hamilton Port Authority, U.S. Steel Canada, the City of Burlington and Halton Region.

Research funding a priority

Getting funding isn't easy for many similar initiatives, Hall said, but Hamilton Harbour has been getting consistent support both locally and from all levels of governments.

One area that should remain a funding priority is research, Hall said.

Thanks to its unique geographic location, Hamilton Harbour has been a favourite subject among researchers, a unique benefit that's uncommon for other water bodies, Hall said.

For example, the Canada Centre for Inland Waters (CCIW), the largest freshwater research facility in the country, is just steps away beneath the Burlington Skyway. Researchers from local institutions like McMaster University, University of Guelph, University of Toronto and Brock University have also studied the harbour at great length.

However, recent cutbacks are threatening this advantage.

CBC Hamilton recently reported that a wave of government cutbacks over the past three years has eliminated at least 20 federal research positions at the CCIW. Some of the centre's remaining top scientists have been re-assigned to study the effects of Alberta's oil sands instead of the Great Lakes.

Environment watchdogs say the change is a threat to the Hamilton Harbour remediation effort.

“We have enjoyed the benefit of a lot of science, a lot of research,” Hall said. “Both Hamilton Harbour and the Great Lakes system as a whole needs to continue to be a priority for that science research because that's the basis of decision-making.”