Nova Scotia's biggest contaminated site will get a federal environmental assessment before the cleanup begins.

The decision was based on submitted comments and the possibility that carrying out the project may cause adverse environmental effects, the federal government said in a news release late Friday night.

Northern Pulp's waste treatment plant at Boat Harbour is scheduled to close in January 2020, as laid out in provincial legislation passed by the Liberals in April 2015.

The pulp mill has said it needs a one-year extension to get a replacement plant up and running because it cannot operate without a treatment facility. Premier Stephen McNeil has refused to extend the deadline of the closure.

The remediation project at the pulp mill effluent site may start in 2021, said Ken Swain, the project's leader, in January.

Swain said the environmental assessment process may delay the cleanup of the wastewater lagoons, where tens of millions of litres of wastewater effluent has been dumped since 1967.

The cleanup project at the lagoons adjacent to Pictou Landing First Nation is also getting a provincial Class 2 environmental assessment, which can take up to 275 days.

Former Nova Scotia environment minister Iain Rankin called the toxic waste lagoons one of the worst cases of environmental racism in Canada.

An aerial view of the Boat Harbour remediation pilot project. (Nova Scotia Government)

Many have also called for a federal environmental assessment of Northern Pulp's new proposed treatment facility — a pipeline that will dump treated effluent from its site in Abercrombie, N.S., into the Northumberland Strait. The plan is undergoing a shorter, 50-day provincial Class 1 assessment.

The company's plan has sparked protests from fishermen, First Nations and the region's tourism industry, who say the plan puts the ecosystem of the Northumberland Strait at risk.

"You can get a federal assessment when you already make a mess, so you should have one before you make one now," said Allan McCarthy of the Northumberland Fishermen's Association.

The Boat Harbour cleanup plan

The Boat Harbour treatment facility is owned by the provincial government, which is on the hook for the cleanup once the facility closes. The cost is forecast at $217 million.

The plan is to dredge up the contaminated sediment at the bottom of the Boat Harbour lagoon and move it to a containment cell.

A pilot project to test dredging techniques was stalled in December because cold weather froze pipes. The pilot project will resume in the spring.

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