The New York State Marine Highway Transportation Company LLC is based in the Port of Troy on the Hudson River. The company connects the Great Lakes and East Coast Ocean Ports through the New York State Canal System.

The Port of Troy Town Dock and Marina is the harbor of refuge for mariners entering and exiting the canal, and it is the point of transfer to Montreal, Amtrak's service to New York City, and the Albany International Airport. The staff at the Port of Troy Town Dock and Marina is available to provide ground transportation, help with cruise destinations, assist in getting parts, or inform visitors about where to find groceries and fine dining.

Port of Troy Town Dock and Marina managers are licensed mariners with 20 years of experience in the business. They have the information mariners need to navigate Lake Champlain, the New York Canal System, and the Hudson River.

The New York State (NYS) Marine Highway Transportation Company has offices, fabrication shops, and storage yards in the Port of Troy to support their marine operations. The company also offers berthing during the navigation season from May through November.

NYS Marine Highway Transportation offers general towing from the Port of Troy between the Great Lakes and East Coast ocean ports. They also offer experience and equipment as well as logistics and transportation for over-sized and overweight project cargoes, specializing in loading and discharging cargo at places with little or no terminal infrastructure.

The Port of Troy's NYS Marine Highway Transportation Company provides ship docking, barge assists, and winter break-outs for marine terminals and ports on the Upper Hudson River including in the Port of Troy, Albany, Rensselaer, Coeymans, Athens, Hudson, Catskill, and Cementon.

The Company provides barge rentals and contractor support for marine, heavy-highway, and drilling contractors. Their services in the Port of Troy include on-site tugs and rental barge deliveries. The NYC Marine Highway Transportation Company also offers salvage equipment (including tugs, barge-mounted cranes, and buoyant devices) to assist grounded and sunken vessels. They raise vessels and remove wrecks.

The US Army Corps of Engineers operates the federally-owned Port of Troy Wharf to moor Coast Guard vessels. Their Port of Troy area office is located at the rear of the wharf. The Troy Wharf has berthing distance of 70.1 meters (230 feet) with alongside depths of 3.4 and 4.3 meters (11 and 14 feet).

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