Formed by the confluence of the Salmon Falls and Cocheco rivers, the Piscataqua River originates at the boundary of Dover, New Hampshire, and Eliot, Maine, and flows southeasterly for 13 miles to Portsmouth Harbor, comprising a partial border between the two states. The last 8.8 miles of the Piscataqua River constitute Portsmouth Harbor, which stretches across New Castle, Portsmouth, and Newington, and the Maine communities of Kittery and Eliot.

Located about 50 miles northeast of Boston, Portsmouth Harbor is the sole deep draft harbor in New Hampshire. It handles about 3.5 million tons of shipping a year for New Hampshire, eastern Vermont, and southern Maine. Items include petroleum products, rubber and plastics, iron and steel scrap, salt, limestone, gypsum, and fish products. The harbor is used by submarines from the Portsmouth Naval Shipyard in Kittery and for fuel deliveries to Pease International Tradeport in Newington. Portsmouth Harbor is also used extensively by a large lobstering fleet, charter fishing vessels, commercial fishermen, excursion boats to the Isles of Shoals situated nine miles offshore, and local and transient boats based at or visiting the nearly 20 boating facilities in the area.

Initial work in Portsmouth Harbor began in 1881. It consisted of:

• Constructing a 1,000-foot-long breakwater between New Castle and Goat Islands. The breakwater, completed in 1881, now serves as a causeway for an access road to New Castle.
• Removing two ledge areas in the middle of the harbor. One area, Gangway Rock, was opposite the western end of the Portsmouth Naval Shipyard, on the New Hampshire side of the channel. Removal of this ledge to a depth of 20 feet began in 1881 and was completed in 1888. The second area was about 0.6 mile upstream, near the southwestern end of Badgers Island, on the Maine side of the channel. Removal of this ledge to a depth of 18 feet began in 1881 and was completed in 1891.
• A 6.2-mile-long channel, 35 feet deep and generally 400-600 feet wide, extending northwesterly from deep water between New Castle and Seavey islands (approximately 2.6 miles from the mouth of the Piscataqua River) to a turning basin located about 1,700 feet past the Atlantic Terminal Sales dock in Newington. The bends were widened to approximately 700 feet by removing ledge at Henderson Point, Gangway Rock, Badgers Island, the U.S. Route 95 Bridge, and Boiling Rock (The small shoal at the U.S. Route 95 Bridge was removed in 1969).This project was completed in 1966.
• Two 35-foot-deep turning basins. The first turning basin is located above Boiling Rock and is 950 feet long. The second is situated at the end of the 6.2-mile-long channel in Newington and is 850 feet long. This project was completed in 1966.

The Corps completed a second project in 1971 that serves a large recreational and small lobstering fleet based in the area of Sagamore Creek, a popular boating center located at the southerly end of Portsmouth Harbor. This work, constructed under Section 107 of the Continuing Authorities Program, consists of:

• A 0.4-mile-long main channel extending from Little Harbor, located immediately south of Portsmouth Harbor between New Castle and Rye, through the Bascule Bridge (Route 1B), then west to the mouth of Sagamore Creek. The channel is six feet deep and 100 feet wide. At Sagamore Creek, the channel forks into northern and westerly channels, described below.
• A 75-foot-wide northerly channel, six feet deep, extending 0.7 mile between Leachs Island and Portsmouth to deep water south of the bridge connecting Shapleigh and Goat Islands.
• A 75-foot-wide westerly channel, six feet deep, extending 0.9 mile up Sagamore Creek to the public landing at the Sagamore Avenue Bridge in Rye. A six-foot-deep anchorage, three acres in area, was constructed at the upper end of the channel.

The swift currents of the Piscataqua River make Portsmouth Harbor one of the fastest flowing commercial port waterways in the northeastern United States.

In 1986 Congress authorized a project that addressed the problems of the harbor’s dangerous navigable conditions. This project included widening the section of channel between the two vertical lift bridges from 600 to 1,000 feet; widening the northern limit of the channel adjacent to Badgers Island by 100 feet; and widening the southern limit of the channel at Goat Island from 400 to 550 feet.

The portion of the improvement project involving widening the channel between the two vertical lift bridges from 600 to 1,000 feet along with the widening of the northern limit of the channel adjacent to Badgers Island by 100 feet was completed in July 1990. The final increment of the project, widening the southern limit from 400 to 550 feet, was completed in April 1992.