[1][2] Originally a tidal estuary, construction of a pulp and paper waste effluent treatment facility in the 1960s led to the pollution of the harbour and the source of ongoing environmental concern.
[4] Since the treatment system began operation in 1967, Boat Harbour has become polluted with dioxins, furans, chloride, mercury and other toxic heavy metals.
Keen to promote economic growth, the provincial government led by Robert L. Stanfield agreed to take responsibility for effluent leaving the mill for a period of 30 years, and turned Boat Harbour into a settling pond by constructing a dam across its mouth.
[14] Within days of the mill's operation, aquatic life began dying and the water level rose by 2–3 m (6.6–9.8 ft),[12] flooding 12 ha (30 acres) of reserve lands.
[12] In 1997, the mill was taken over by Kimberly-Clark and in 2003 they agreed with the Band to extend treatment beyond the 2005 deadline, by piping effluent directly from the aerated settling pond to the Northumberland Strait where it would be released on the ebb tide, and to return Boat Harbour to a tidal state.
However, the mill was purchased in 2004 by Neenah Paper who were not inclined to spend capital on water treatment, and following concerns from the Department of Fisheries and Oceans over the environmental consequences of the pipeline, that plan was cancelled in 2005.
Following that government's decision to provide $90 million assistance to the mill to purchase woodland and improve air treatment systems but do nothing about Boat Harbour, the First Nation filed an action in the Nova Scotia Supreme Court.
[30] Northern Pulp was permitted to continue to use the Boat Harbour wastewater treatment plant until the end of April 2020 as it prepared the facility for indefinite closure.