The City of Groton Harbor Management Commission is responsible for planning and operating the Port of Groton. The Port of Groton waterfront stretches on the east side of the Thames River estuary for about six kilometers to the estuary's mouth.

The Groton Bank area is the oldest part of the Port of Groton and the town, and it contains much of the city's historic buildings as well as several marinas and docks for fishing and charter boats. The industrial area of the waterfront contains facilities owned by three major firms: the Electric Boat Corporation, Pfizer, and the Amerada Hess Corporation's oil terminal. This area also comprises the heart of southeastern Connecticut's industrial sector and employment. The Thames Estuary shorefront is a largely residential area with a golf course and city-owned waterfront park. This shorefront area also contains two piers for recreational fishing and sightseeing as well as the city-owned Eastern Point Beach and the privately-owned Shennescossett Beach Club.

From Pine Island Bay to the east of Avery Point in the Port of Groton, the waterfront includes the pier of the University of Connecticut and several major boating faculties that include the Shennecossett Yacht Club, Pine Island Marina, Connecticut's Bayberry Lane boat launch. The Port of Groton's most important mooring area is in Pine Island Bay, which is the most active area for recreational boating.

The Baker Cove area in the Port of Groton contains the state-owned Groton-New London Airport and residential areas with small water-related businesses. The Cove is very shallow, allowing navigation for small boats only. This Port of Groton cove's low marshy shores are a major natural resource for the area. Public access to the marshes is available at Jupiter Point Road. Where the Cove narrows to Birch Plain Creek, a city-owned conservation area of salt marshes is part of a city-owned open space used for teaching and passive recreation.

The Port of Groton is located on the New London Harbor, and the port's entry channel is about 12 meters deep as far north as the Electric Boat Corporation's property. Federally-maintained buoys mark the entrance to Pine Island Bay. A natural channel provides entrance to Baker Cove.

There are no major anchorages in the Port of Groton outside the mooring areas for small boats. There are about 76 commercial boats slips in the Port of Groton. In 1972, the Pine Island Marina and the Shennecossett Yacht Club established a grid layout for small boats in the bay that maximized the limited anchorage available in the bay. The Pine Island Marina provides access to moorings for the general public, which is the most important mooring area in the Port of Groton. Under direction of the Port of Groton Harbormaster, the Yacht Club and Pine Island Marina maintain the mooring grid. Of the total 228 moorings in Pine Island Bay in 2005, the Shennecossett Yacht Club has 39, the Pine Island Marina has 70, and there are 119 moorings available for the general public.

Marinas containing boat slips are located in the Thames Street area, Baker Cove, and Pine Island Bay. Unfortunately, most of the privately-owned slips are in poor condition and can accommodate a grand total of six boats.

Recreational fishing and boating are popular activities in the Port of Groton. Shore-based fishermen and fishermen in small boats are a common sight in Port of Groton waters. There are also several fishing charter operations in the city. Much of the Port of Groton area supports a recreational and commercial lobster fishery, and at least ten commercial lobster operations are active in the New London Harbor and the Port of Groton. Unfortunately, water quality in the Port of Groton does not support recreational and commercial bi-valve shell fishing. Blue crabs can still be harvested in Baker Cove.

The Port of Groton is proud to be the home of the Naval Submarine Base New London (SUBASE), the US Navy's first submarine base and the "Home of the Submarine Force." Almost every officer and sailor in the submarine force will be assigned to the base sometime during their military career. The Submarine Force Library and Museum and Historic Ship Nautilus exhibit are major attractions in the Port of Groton. Located on the east side of the Thames River in the Port of Groton, the base is home to over 40 tenant commands, the Submarine School, and the Naval Submarine Support Facility. The base is home to 21 attack submarines and the US Navy's nuclear research deep submersible unit. The base is home to some ten thousand active duty and civilian workers.

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