Environment Canada filed the charges under the Fisheries Act after raw sewage from a combined overflow pipe near Brockton Point poured into waters around Stanley Park.
Under heavy rain conditions, combined sewer pipes can get backed up and raw sewage ends up bypassing filtration plants and flowing into natural water sources.
The sentencing hearing has revealed that conditions were dry and highlighted the errors that saw more than 3,000 barrels of raw sewage released off Brockton Point.
The district has agreed to pay $5,000 in fines and contribute $100,000 to an environmental damages fund.
Sentencing is still underway and the court has yet to deliver a final decision.
At the time of the incident, environmental groups said they hoped the charges would alert the public to what they claim is an ongoing problem.