Lewis and Clark explored this area in 1805-1806. Early settlements were established by fur traders as early as 1810. As American immigration increased in the mid-1840s, lasting settlements began to appear. The Yakima Indian War (1855-1859) drove many Washington Territory residents south of the Columbia River and helped boost the populations of St. Helens and Columbia City.

The first district court met in 1854 in Milton, which served as the county seat until 1857 when it was moved to St. Helens. St. Helens was founded in 1848 and took its name from the nearby Mt. St. Helens. The present courthouse was built in 1906, and an annex was constructed in 1968. Most county offices are now housed in the annex.

Columbia County had a county court form of government until 1971 when a board of commissioners was elected. The 2009 population of 48,410 represented a 11.1% increase over 2000.

The primary industries of Columbia County are timber, fishing, water transportation, dairying, horticulture, and recreation. The extensive stands of old growth timber, which had attracted many of the early settlers to the area, were completely logged over by the 1950s. Second growth timber provides the raw material for local lumber and paper mills. The Trojan Nuclear Plant, located near Rainier, was in operation from 1975 to 1993.