The NPCA is upgrading an earlier Lake Erie Flood Watch.
South Niagara remains under a wind warning, with winds of up to 100 km/hr expected later today.
The Niagara Peninsula Conservation Authority says water levels could rise by 1.6m or 5.25ft above current water levels in Lake Erie during the storm.
Significant wave heights are expected to be in excess of 2m or 6.5ft meaning flooding of low-lying areas is expected due to storm surge and the significant wave uprush.
Damage to the shoreline is also likely during this event.
Water levels should start to recede through the early morning hours of Thursday.
The city of Port Colborne is preparing for the storm by closing off some waterfront areas.
The NPCA says today's weather will be similar in magnitude to the storm that occurred recently on Halloween night which knocked out power to thousands and even shifted the Niagara Falls scow.
Residents living along Lake Erie should take appropriate precautions such as closing storm shutters and flood-proofing low openings in their homes.
They are being asked to stay away from the shoreline of Lake Erie during the event.