Falmouth Harbor's Waterways Committee is charged with protecting, maintaining, and improving the area's navigable waterways and public resources. Specifically, the Committee advocates for users of the waterways, maintains and improves waterway resources, creates new waterway resources and oversees project construction, secures financing for waterway projects, and develops the rules regulating waterway facilities.

The Falmouth Harbor Master Department manages and patrols the 14 harbors, about three thousand moorings, about 70 miles of Falmouth Harbor coastline, and the Falmouth Town Marina in the inner Falmouth Harbor. Falmouth Harbor Master Department has an 8.2-meter (27-foot) Boston Whaler patrol boat, an 8.2-meter (27-foot) Metal Shark patrol boat, a 7-meter (23-foot) Edgewater patrol boat, a 6.4-meter (21-foot) Eastern patrol and pump-out boat, and several small boats used for the Falmouth Harbor marina.

Falmouth Harbor actually includes many different harbors. Magansett Inner Harbor offers deep-draft access, and it is the harbor closest to the Cape Cod Canal. Other deep-draft harbors include Quissett Harbor, Great Harbor at Woods Hole, Eel Pond at Woods Hole, Little Harbor at Woods Hole, and Falmouth Inner Harbor (offering transient slips from April through November). The remaining Falmouth Harbors offer shallow-draft and limited draft access.

Falmouth Harbor is home to the Falmouth Town Marina. The main marina offers a total of 66 slips with depths ranging from almost 26 meters (85 feet) to 7.6 meters (25 feet). There is only 26-meter slip. There are five 16.8-meter (55-foot) slips, twenty-four 13.7-meter (45-foot) slips (12 on a transient float), twenty-four 10.7-meter (35-foot) slips, and twelve 7.6-meter (25-foot) slips in the Falmouth Harbor Marina.

The Falmouth Harbor Marina's Charter Boat Section contains eight slips for boats to 15.2 meters (50 feet) in length. The Robbins Road Floating Docks in Falmouth Harbor contain fourteen slips for vessels to 10.7 meters (35 feet) and eight for vessels up to 7.6 meters (25 feet). Two slips at the Falmouth Harbor's Robbins Road Fixed Docks can accommodate vessels to 10.7 meters (35 feet).

The Davis Marine Park Bulkhead, which is a flat wall tie-up in Falmouth Harbor rather than a slip, can accommodate two overnight transient vessels of up to 24.4 meters (80 feet) in length. The Tides Bulkhead in Falmouth Harbor, which is also a flat wall tie-up, can accommodate five overnight transient vessels of up to 76.2 meters (250 feet) in length.

The Falmouth Harbor Marina offers a variety of services that include a boat launching ramp, a pump-out station, restrooms, and showers. Most slips at Falmouth Harbor's main marina and at the Robbins Road Floats have cable TV hook-ups. All areas have fresh water hook-ups, and most areas have 30/50 amp electric service. Limited 100 amp service is also available.

The Woods Hold, Martha's Vineyard, and Nantucket Steamship Authority was created by the State legislature to assure appropriate transportation for people and cargo on the islands of Nantucket and Martha's Vineyard. Falmouth Harbor and Hyannis have mainland landings for the ferries. Private ferry operators are licensed to provide services. The Authority operates freight vessels that link shipping of commercial goods to the islands that are not otherwise transported by air.

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