Irving Pulp and Paper has pleaded guilty to three counts of effluent discharge from its west side pulp mill into the Saint John River.
In a statement on Tuesday, the company said it will pay a $3.5-million penalty, with one-third dedicated to wild Atlantic salmon research and conservation.
The proposed court agreement would also require the company to install a multimillion-dollar effluent treatment facility as an operating condition.
Irving said federal authorities acknowledged there was no evidence of any fish mortality, but the company did fail a required test of rainbow trout survival in the effluent.
The company previously pleaded not guilty to 15 counts of illegal dumping into the river over a two-year period between June 2014 and August 2016.
Irving has said the charges were based on fish mortality rates in a lab test, adding none of the incidents which led to the charges caused any environmental damage or fish deaths in the natural environment.