The Wenonah Park Wharf in the Port of Bay City is operated jointly by the city and the US Environmental Protection Agency (EPA) to moor Agency vessels as well as to occasionally land passengers on excursion vessels and small craft. The EPA's R/V Lake Guardian and R/V Hydra are moored at the upper section of this Port of Bay City wharf. At the rear of the wharf are a city park and city parking lots. The Port of Bay City's Wenonah Park Wharf has berthing space of 350.5 meters (1150 feet) with alongside depths of 4.3 and 4.9 meters (14 and 16 feet).

Although it was not in use at the time of the survey in 1996, the Port of Bay City's Parcel No. 10 Dock is owned by the city. Formerly used to receive stone, lime, and salt, the city plans to develop the dock for non-heavy industrial uses. The Port of Bay City's Parcel No. 10 Dock has berthing distance of 325.5 meters (1068 feet) alongside depth of 6.7 meters (22 feet). The Port of Bay City's Parcel No. 9 Dock was not in use at the time of the survey, the city planned to develop it for non-heavy industrial uses as well. The Port of Bay City's No. 9 Dock has berthing distance of 143.3 meters (470 feet) with alongside depths of 3.7 and 4.6 meters (12 and 15 feet).

The Port of Bay City Wharf is owned by AJ Fisher and operated by Bay Aggregate Inc. It is used to receive stone, coal and coal coke, lignite, fertilizers, and sand and gravel. Open storage at the rear can accommodate 100 thousand tons of stone and 25 thousand tons of sand. An electric conveyor belt connects the open storage area to a ready-mix concrete plant at the rear of the wharf. This Port of Bay City wharf has berthing distance of 262.1 meters (860 feet) with alongside depth of from 3.7 to 6.1 meters (12 to 20 feet).

AJ Fisher owns, and Bay Aggregate Inc. operates the IB Industrial Park Wharf in the Port of Bay City to receive stone. There are three private warehouses at the rear, and the open storage area has capacity for 50 thousand tons of stone. The Port of Bay City's IB Industrial Park Wharf has berthing space of 402.3 meters (1320 feet) and alongside depths from three to 3.7 meters (10 to 12 feet).

The Fletcher Oil Company owns the Fletcher Marine Terminal's Ship Wharf in the Port of Bay City. One surface track serves the rear tank-car-unloading rack and connects with the Central Michigan Railway. The wharf was used on a stand-by basis at the time of the survey, and this Port of Bay City wharf has been used to process coal and coal coke, lignite, fertilizers, limestone, dredged materials, sand and gravel, and sulfur. A pipeline connects the terminal to a fertilizer storage tank at the rear with capacity for 4.3 million gallons. A second pipeline connects the wharf to truck-loading racks at the rear of this Port of Bay City wharf, which has berthing distance of 79.2 meters (260 feet) with alongside depth of 7.6 meters (25 feet).

The Fletcher Marine Terminal also operates the Tugboat Wharf in the Port of Bay City to moor tugboats and other small craft. This Port of Bay City wharf has berthing distance of 57.3 meters (188 feet) and alongside depth of 3.7 meters (12 feet).

The Wirt Transport Company owns and operates the Port of Bay City Stone Dock to receive stone, salt, and coal and to occasionally ship stone by barge. An open storage area at the rear of the Dock can accommodate about 220 thousand tons of dry bulk cargoes. The Port of Bay City Stone Dock has berthing space of 762 meters (2500 feet) with alongside depth of 7.6 meters (25 feet).

To allow Port of Bay City residents to move across the river while also letting large vessels pass, the Port of Bay City has four drawbridges that operate 24 hours a day from the March 16 to December 15 shipping season. These include the Independence Bridge, the Liberty Bridge, the Veterans Memorial Bridge, and the Lafayette Bridge. These Port of Bay City bridges are generally open from 6:30 to 8:30 am and from 3:30 to 5:30 pm except for weekends and holidays. From the December 16 to March 15 non-shipping season, 12-hour notice is required for a bridge to be opened.

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