Long before Europeans ventured across the Appalachian Mountains, Indians were plying the inland rivers in various types of boats, the most notable being the bark canoe. Made of birch, hickory, or elm bark, these ranged from small two-person canoes to much bigger boats capable of carrying more than a dozen men and heavy cargo. Other vessels used by the Indians were dugout canoes made of tree trunks that had been hollowed out by fire and ax. The bark canoe was easily transportable, readily repaired, and could be used as a shelter on land, if needed. The dugout canoe was heavy, awkward, and was not taken from the river.

Early settlers found these Native boats useful, and both dugout and bark canoes were extensively adapted for trade and travel. A variety of other vessels were developed to carry heavier commerce. The most popular were the keelboat and flatboat.

Keelboats were usually 60 to 80 feet long and 15 to 20 feet wide. Constructed with a shaped bow and stern and a keel running the full length of the deep hull, they were used to transport passengers and freight both upstream and downstream. Going downstream the boat floated with the current, but moving upstream required six to 18 men setting pike poles in the bottom of the river and pushing against the pole while walking the length of the boat. Keelboats operated from the 1780s until about the beginning of the Civil War.

There were many varieties of boats referred to as flatboats, all more primitive than keelboats. These traveled only downstream and were torn apart when they reached their destination, to be used locally as building material. Known as flatboats, Kentucky boats, Orleans boats, or broadhorns, according to certain design differences, these boats were roughly built, box-like vessels ranging up to 90 feet or longer by 20 to 24 feet wide. Floating downstream, steered by heavy long paddles and a rudder, the flatboat came to be known as the "Ark of the Empire" because of the number of immigrant families and the amount of Ohio Valley products such boats moved to the west and to New Orleans. Flatboats were used to ship bulk products downstream until after the turn of the 20th century.

In 1811, the first steamboat on the inland rivers was launched on the Ohio River at Pittsburgh. Named the New Orleans, it was followed by thousands more. Significant improvements in steamboat design were made in the Washington, launched at Wheeling in 1816. Steamboats would be the major mode of river transportation until well into the 20th century. By the 1830s, there had been improvements in the design and construction of the sidewheel and sternwheel boats and their steam engines, and 450 boats operated on the Ohio River and its tributaries. Extensive navigation improvements to the rivers were begun during this period and continue to the present.

In West Virginia steamboats operated on the Big Sandy, the Kanawha and Little Kanawha, the Ohio, Monongahela, and even on a short stretch of the New River at Hinton. There were three major types of steamboats: the packetboat, carrying passengers and limited freight between cities and towns; ferryboats, carrying passengers and light vehicles across streams; and towboats that were used to push sometimes large fleets of barges loaded with bulk raw materials. There were several variations of these vessels, including excursion boats, showboats, and raftboats.

Steamboats were the major means of passenger transportation within the Mississippi River basin until after the Civil War and competed successfully with trains until the 1920s. Between the 1920s and 1930s, packetboats disappeared from inland rivers, while towboats were improved by being constructed of steel and powered with diesel engines and propellers. Larger barges made of steel replaced the old wooden barges.

The Marietta Manufacturing Company of Point Pleasant made barges, tugs, and other river craft from 1916 to 1970. During World War II, it also built four Navy net tenders, 16 Army mine planters, and 53 Army landing tugs, while employing as many as 2,200 workers

Today's modern towboats equipped with radar, sonar, satellite communications systems, and licensed personnel provide the nation with the cheapest method of transportation available for the shipment of bulk commodities, including West Virginia coal. Rivers remain important for the movement of bulk goods. At present the Ohio, Monongahela, Big Sandy, and Kanawha are all used for river navigation. Hundreds of millions of tons of cargo are shipped on these streams each year. Coal and coke are the leading commodities moved by water in West Virginia, followed by petroleum, sand and gravel, and chemicals. Huntington is the country's largest inland port, based on tonnage shipped.

Passenger travel is a thing of the past on West Virginia waters, and excursion boats have had mixed success. The P. A. Denny, which operated for many years on the Great Kanawha River, departed Charleston in 2004. The Blennerhassett Island fleet runs visitors from Parkersburg to the Island and back. There have been excursion boats at Huntington, Wheeling, and other towns, but none has been successful for more than a few years.