The Port of Lewiston is part of the Columbia-Snake River System called The Inland Marine Transportation System, and it is managed by the U.S. Army Corps of Engineers. The Port of Lewiston is located at the inland terminus of the river system. It offers a sensible alternate route for shipping goods to Canada and the Midwest United States.

There are four dams on each of the rivers, totaling eight dams and locks that help vessels move upstream and downstream between the Port of Lewiston and Portland/Vancouver. These locks move vessels some 222 meters (730 vertical feet) from the coastline to the Port of Lewiston. The 4.3-meter (14-foot) river channel can accommodate loaded barges with an average 3 meters (10 feet) of draft and tugs with from 3.4 to 3.7 meters (11 to 12 feet) of draft.

Voters of Nez Perce County created the Port of Lewiston in 1958. The Lewiston Port Authority is charged with overseeing harbor operations and terminals, participating in the city's industrial and economic development efforts, and international trade. One of the Port of Lewiston's main goals is to promote economic growth to put the city in a competitive position in the regional economy. The Port of Lewiston's waterfront property and location of the business office is Northport.

As an inland port, the Port of Lewiston offers the full range of transportation modes to port shippers. On water, scheduled tug services tow container barges, navigating through the eight dams and locks for some 50 hours, between Portland and the Port of Lewiston.

Located adjacent to US Highway 12, the Port of Lewiston has direct links to Montana to the northeast. Highway 95 and US-84 offer access south to Boise. US 90 to the north links the Port of Lewiston to Spokane Washington. The Port of Lewiston is connected to the Burlington Northern Santa Fe and Union Pacific Railroads, and the Nez Perce County Regional Airport is just two miles south of the port.

In 1975, container barge serves started on the Columbia River. In 1978, the Port of Lewiston started shipping containers by barge to Portland. That first year, over 507 TEUs were transported from the Port of Lewiston. Tug and barge services continue to provide consistent service to deliver containerized cargo to ocean-going vessels in Portland.

The dock at the Port of Lewiston is 38.1 meters (125 feet) long. Just 400 meters (1.3 thousand feet) from US Highways 12 and 95, the Port of Lewiston dock can handle any roll-on/roll-off loads that would be allowed on Idaho highways.

The Port of Lewiston's on-site facilities include the Container Terminal Dock, Inland 465 Warehousing & Distribution, Lewis-Clark Terminal Dock, and CLD Pacific Grain Elevator Dock. The main export cargo for the Port of Lewiston is grain. The Port of Lewiston has a total capacity for 6.2 million bushels at the Lewis Clark Terminal and CLD Pacific Grain facilities.

The Port of Lewiston has over 1.8 thousand square meters (20 thousand square feet) of warehousing. Cargo movements is facilitated by a 240-ton mobile crane, three 35-ton container lift trucks, three 4-ton forklift trucks, and one 15-ton forklift truck in the Port of Lewiston.

Adjacent to the Port of Lewiston's container yard is a 13.9 thousand square meter (150 thousand square foot) distribution facility operated by Inland 465 Warehousing and Distribution. This Port of Lewiston facility has ten truck bays and five bays for rail tracks connecting to both the Union Pacific and Burlington Northern Santa Fe Railroads. Outside and inside storage is provided for paper and forest products, agricultural products, and manufactured goods.

Facilities at the Port of Lewiston distribution facility include 10 truck bays, 5 rail bays (served by Burlington Northern/Santa Fe and Union Pacific). There are also controlled temperature inside and open outside storage for forest and paper products, manufactured goods, and agricultural products in the Port of Lewiston.

The Port of Lewiston started working with US and Canadian companies in 2008 to ship over-sized cargo. Refinery equipment leaves the Port of Lewiston destined for the Kearl Oil Sands in Alberta Canada. Wind-powered generators leave the Port of Lewiston destined for Midwest region of the United States and for coal-fired electrical plants in Wyoming. There are more than 20 acres of storage next to dock facilities for over-sized cargo in the Port of Lewiston.

Adjacent to State Highway 128 connecting with US 12, the Harry Wall Industrial Park is also next to Northport, facilitating intermodal operations. The Port of Lewiston industrial park consists of 117 acres for light to heavy industry.

Covering 24 acres, a new business and technology park was constructed to support modern business and technology companies. Planned to expand to 44 acres, the Port of Lewiston worked with the City and Nez Perce County to build infrastructure and utilities for the new park.

The Continental Grain Company owns and operates the Port of Lewiston Elevator Dock. The dock is served by one surface rail track with capacity for six rail cars that connects with the old Camas Prairie Railroad (Burlington Northern Santa Fe). Used to ship grain, this Port of Lewiston dock has ten concrete silos in the rear with capacity for 500 thousand bushels of grain. The Elevator Dock has berthing space of 106.7 meters (350 feet) with alongside depth of 4.3 meters (14 feet) NPE.

The Lewis-Clark Terminal, located at the Port of Lewiston Dock, has two surface tracks with total capacity for 12 rail cars that connect with the Camas Prairie Railroad. Also used to ship grain, the Port of Lewiston's Lewis-Clark Terminal has 28 concrete silos and a steel storage building with capacity for over 5.2 million bushels of grain. The Lewis-Clark dock has berthing space of 106.7 meters (350 feet) with alongside depth of 4.6 meters (15 feet) NPE.

The Longview Fibre Company owns, and the Mountain Fir Chip Company operates the Port of Lewiston Division Dock. Used to ship wood chips and hogged fuel, storage bins at the rear of the dock can store 4.5 thousand BDUs of wood chips. The log processing plant at the rear can store 8.5 million board-feet of logs. The Port of Lewiston's Division Dock has berthing space of 61 meters (200 feet) with alongside depth of 5.8 meters (19 feet) NPE.

The Container Terminal Dock is owned by the Port of Lewiston and operated by Gator Intermodal. One surface track links the terminal to the Camas Prairie Railroad. The Port of Lewiston Container Terminal Dock is used to ship and receive containerized and conventional general cargo, paper products, and lumber. The Port of Lewiston Container Terminal Dock has berthing space of 91.4 meters (300 feet) with alongside depth of 5.5 meters (18 feet) NPE.

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