Port facilities in Manitowoc Harbor are governed by the nine-member Board of Harbor Commissioners. Serving three-year terms, they control the commercial aspects of operations of Manitowoc Harbor and public harbor facilities. The Board of Harbor Commissioners for Manitowoc Harbor is authorized to operate public wharf and terminal facilities and equipment, operate public railroad beltlines and facilities, assign berths at Manitowoc Harbor facilities, and maintain guards at public harbor facilities. The Board of Harbor Commissioners also operates municipal airport facilities on or next to harbor lands, operates municipal harbor craft, and acquires vessels for use in commerce.

Manitowoc Harbor is a federally-authorized port. The city maintains the channel extension and, working with the US Army Corps of Engineers, maintains a channel depth of 6.4 meters (21 feet). Manitowoc Harbor is a member of the Wisconsin Commercial Ports Association. Working with the Manitowoc Planning Department, the Manitowoc Harbor Board of Commissioners approves the 3-Year Harbor Plan covering capital projects for harbor improvements and oversees the administration lease for the Manitowoc Marina.

The Manitowoc Marina is a state-of-the-art full-service complex that provides dependable personalized professional services to the Manitowoc Harbor boating community. The Manitowoc Harbor marina has 250 deep-water slips including guest slips and offers maintenance and repair services and both indoor heated and outdoor boat storage. The ship's store carries varied merchandise that includes clothing, parts, boating accessories, and nautical gifts.

Moorage services include a launch ramp, free pump-outs, private restrooms and showers, dockside water and electricity, a private lounge, and free parking. Slips up to 15.2 meters (50 feet) in length are available for annual, monthly, weekly, and daily rental. Dry summer storage is available, as is winter storage. Outdoor winter storage includes pressure bottom washing, haul-out and launch with the Travelift, cradle or trailer storage during the boating season, and a week's free dockage before and after the storage period. Indoor heated storage is also available in a 2.2 thousand square meter (27 thousand square foot) building from mid-September through mid-June. Customers who use indoor heated storage services have the same benefits as listed for outdoor storage. Mast storage is also available for boats in storage at the Manitowoc Harbor marina.

The current 3-Year Harbor Plan for Manitowoc Harbor includes several improvement projects. Manitowoc Harbor plans to reconstruct and dredge 237.7 meters (780 feet) along Manitowoc River to prevent erosion of the river bank, allow for dredging a deeper channel, and allowing a riverfront to build, service, and launch larger yachts. The plan includes the removal of two inactive railroad bridges that are no longer used by the Canadian National Railroad to improve access to the river and the inner harbor waterway and to increase safety for ships and yachts moving further upriver.

The Manitowoc Harbor 3-year plan also includes rehabilitating and enhancing 198 meters (650 feet) of dock wall and its landward side to facilitate transloading operations. Another project aims at improving public access to and amenities at the lakefront. It involves building and rehabilitating the dock wall and slip at the lakefront city-owned car ferry dock by adding 304.8 meters (1000 feet) of steel sheet piling and by dredging about 7.6 thousand cubic meters (10 thousand cubic yards) of bottom sediment. This project includes upgrades to dock, slip, and rail. This project would allow Manitowoc Harbor to expand its links to commercial lake services handling passengers and trucks and to provide additional commercial dock and warehouse space.

Manitowoc Harbor will also repair a 305-meter (1000-foot) area of dock at the site of a former cement transloading property and dredging the river to accommodate larger ships. The repairs would encourage re-use of this currently under-used harbor space site for higher uses in Manitowoc Harbor.

Lake Michigan Carferry Service Inc. owns and operates the Manitowoc Harbor Carferry Slip and the SS Badger to transfer passengers and cars to and from car ferries that travel to/from Ludington, Michigan. The Manitowoc Harbor Carferry Slip has berthing distance of 125 meters (410 feet) with alongside depth of 5.5 meters (18 feet).

The City of Manitowoc owns and operates the Manitowoc Harbor City Dock for mooring vessels. The paved area at the rear of this Manitowoc Harbor dock is used for parking. The City Dock in Manitowoc Harbor has berthing distance of 89.3 meters (293 feet) with alongside depths of 2.1 and 2.7 meters (seven and nine feet).

The City of Manitowoc owns and operates the Maritime Museum Wharf in Manitowoc Harbor to moor excursion vessels and the USS Cobia exhibit. ¬The Maritime Museum Wharf in Manitowoc Harbor has berthing distance of 106.7 meters (350 feet) with alongside depth of four meters (13 feet).

The Manitowoc Company owns and operates Berths A and B in Manitowoc Harbor to ship heavy machinery and to moor vessels. A fabrication shop is located at the rear of Berth A, and there is an open storage area at the rear of Berth B. Rail tracks serve the plant at the rear and connect with Wisconsin Central, a subsidiary of the Canadian National Railway. Berths A and B have berthing distance of 137.2 meters (450 feet) with alongside depth of 6.4 meters (21 feet) and 207.3 meters (680 feet) with alongside depths of 4.9 and 5.5 meters (16 and 18 feet).

The Manitowoc Company owns and operates Berths B-A and C in Manitowoc Harbor to ship heavy-lift items and moor vessels. ¬Rail tracks at the plant connect with Wisconsin Central. Berths B-A and C have berthing distance of 79.2 meters (260 feet) with alongside depths of 4.3 and 4.9 meters (14 and 16 feet) and 109.7 meters (360 feet) with alongside depths of 4.3 and 4.9 meters (14 and 16 feet).

The Manitowoc Company owns and operates Berth J in Manitowoc Harbor to moor vessels. The Downtown Storage Yard is located at the rear of the dock. Manitowoc Harbor's Berth J has berthing distance of 289.6 meters (950 feet) with alongside depth of 2.7 meters (16 feet).

The Manitowoc Company owns and operates Berths G and H in Manitowoc Harbor to moor vessels. Rail tracks serve the plant at the rear of the berths and connect with Wisconsin Central. Manitowoc Harbor's Berths G and H have berthing distance of 144.8 meters (475 feet) with alongside depths of four and 6.7 meters (13 and 22 feet) and 82.3 meters (270 feet) with alongside depth of 5.5 meters (18 feet).

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