Port Cape Charles is a United States port-of-entry. The modern Port Cape Charles is a commercial port and the terminus of the Eastern Shore Railroad. Tugboats and barges are the main vessel traffic at Port Cape Charles, although the municipal marina provides berthing for transient recreational boaters. Port Cape Charles continues to be a busy commercial area with little room for maneuvering, so smaller vessels must yield to the large commercial vessels using the port.

The municipal bulkhead is at the north basin at Port Cape Charles harbor's east end. While the north basin is a designated Harbor of Refuge, anchorage is not allowed in the basins or the outer Harbor Basin.

Crossing the Chesapeake Bay, the rail ferry service between Port Cape Charles and Norfolk is one of only two such services still operating in the United States. Tugboats move two barges with capacity for 15 and 25 cars across the route. In 2006, the Eastern Shore Railroad was acquired by Cassatt Management, which operates the service today as the Bay Coast Railroad. The Bay Coast Railroad connects Port Cape Charles with the Norfolk Southern Railway at Norfolk and at Pocomoke City in Maryland.

From the time it began operating, the Port Cape Charles rail ferry service has been a profitable enterprise, creating an economic boom on the Delmarva Peninsula from the late 19th Century until the Great Depression. After World War II, the rise in automobiles caused passenger use at Port Cape Charles to decline. Passenger service was discontinued in 1958.

The northern portion of the Bay Coast rail system connects the Norfolk Southern in Pocomoke City to Port Cape Charles where a car float crosses the Chesapeake Bay. Its southern terminal at Little Creek, Virginia, connects with the CSX Transportation, Norfolk Southern Railway, and the Norfolk and Portsmouth Belt Line Railroad.

Port Cape Charles Harbor is managed by the Harbor Master. Port Cape Charles has depths from 2.1 meters (seven feet) at the Inner Harbor entry, the fuel dock, and the slips. The West Harbor has 5.5-meter (18-foot) depth at the dock entry and dockside.

The Municipal Corporation of Cape Charles Harbor hosts industrial, commercial, and recreational vessels in its protected basin. The basin contains almost 427 meters (1400 feet) of dock space and 51 slips. The Port Cape Charles harbor offers boat ramps for sport fishing and pleasure craft and for charter boats that run daily fishing expeditions in the Chesapeake Bay. The Port Cape Charles harbor also provides deep-water slips and docks within walking distance of the Historic Town. The Port Cape Charles has been designated a "Virginia Clean Marina."

The non-segregated Port Cape Charles harbor facility serves local companies using the docks to move their products to and from the Eastern Shore. The Municipal Corporation of Cape Charles Harbor serves all people who use or work at Port Cape Charles Harbor, while the Harbor Master protects the property of Port Cape Charles users and charges fees for harbor use. Port Cape Charles Harbor policies limit the number, size, and use of vessels using Port Cape Charles.

Owned by Port Cape Charles and operated by the Harbor Master, office hours at the Port Cape Charles Harbor are 8am until 5:30pm every day, although after-hour arrivals are permitted with advance notice. A-Dock in Port Cape Charles has three berths with berthing distance of 38.1, 41.1, and 48.8 meters (125, 135, and 165 feet). The berths are equipped with 50- and 100-amp power. B-Dock in Port Cape Charles has twelve berths and the T-head. Slips have 50-amp power, and the T-head has berthing distance of 36.6 meters (120 feet) and has both 50- and 100-amp power. Port Cape Charles' C-Dock and D-Dock have 16 slips each with 30- and 50-amp power.

Port Cape Charles is implementing improvements to harbor infrastructure. The Port Cape Charles Offshore Breakwater Project involved adding two 122-meter (400-foot) sections of breakwater.

Southport Investors is seeking funding for the planned Port Cape Charles Yacht Center. Port Cape Charles is ideally located between Florida and the Northeast as a stopping point for manufacturing, sales, and repair of yachts. The new Port Cape Charles yacht center will have three floating docks, two travel lift piers, and a pad at the southeast end of the harbor next to the Coast Guard station. A 183-meter (600-foot) floating dock will be adjacent to the south harbor bulkhead. The waterfront will have a walkway and a stone-surface boatyard. The new Port Cape Charles center will include a repair shop, multi-rack dry storage, fuel tanks, a washing system, and a SaniSailor vacuum system for pump-outs.

Port Cape Charles' Bay Creek Marina is a full-service resort. The marina has 124 floating cushioned single loading slips with no overhead obstructions that can accommodate vessels to 45.7 meters (150 feet). Open to the public, marina amenities and services include electricity, water, cable TV and wireless Internet, fuel, and sewer pump-out. This Port Cape Charles marina has luxury bathrooms with lockers and showers, a swimming pool, laundry facilities, and a trash area. Slips at the Port Cape Charles Bay Creek Marina are available for long- and short-term lease and transient rental (including weekends and holidays).

The Bay Creek Marina in Port Cape Charles has two 18-hole Signature golf courses designed by Jack Nicklaus and Arnold Palmer. It also boasts many walking trails, a private beach, and a vintage dining excursion railcar. The marina also has condominiums, homes, and suites for those who prefer a longer stay.

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