The source of the river is a spring called Humboldt Wells at the northern tip of the East Humboldt Range, just outside the city of Wells. The river flows west-southwest through Elko County past the community of Elko. In northern Eureka County it passes along the south end of the Tuscarora Mountains, and then along the north end of the Shoshone Range. At Battle Mountain it turns northwest for approximately , then west at Red House and past Golconda and a spur of the Sonoma Range. Then it turns southwest, flowing past Winnemuca and through Pershing County, along the western side of the Humboldt Range and the West Humboldt Range. It empties into an intermittent lake in the Humboldt Sink on the border between Pershing and Churchill counties, approximately southwest of Lovelock.
The river receives the North Fork of the Humboldt River in Elko County, approximately upstream from Elko, and the South Fork approximately downstream. It merges with the Reese River near Battle Mountain, and receives the Little Humboldt River approximately upstream from Winnemucca. It is impounded in central Pershing County by the Rye Patch Dam, forming the Rye Patch Reservoir.
The river is highly variable in flow, generally decreasing in volume downstream to the west, in part due to the removal of water from the river for irrigation.
The region of the river in northern Nevada was sparsely inhabited by the Paiute and Shoshone at the time of the arrival of European American settlers. The region was little known by non-indigenous peoples until the arrival of fur trappers in the middle 19th century.
The first recorded sighting of the river was on November 9, 1828, by Peter Skene Ogden during his fifth expedition to the Snake Country. Odgen came southward along the Little Humboldt, encountering the main river at the confluence near Winnemucca. Ogden explored the river for several hundred miles, blazing a trail along it and making the first known map of the region. He initially named the river "Unknown River", due to the source and course of the river still being unknown to him, and later "Paul's River", after one of his trappers who died on the expedition and was buried on the river bank. He later changed it again to "Mary's River," named after the Native American wife of one of his trappers, which later somehow became "St. Mary's River". However in 1829 he suggested that "Swampy River" best described the course he had traversed. In 1833 the Bonneville-Walker fur party explored the river, naming it "Barren River". Washington Irving's 1837 book describing the Bonneville expedition called it "Ogden's River", the name used by many early travelers. By the early 1840s the trail along the river was being used by settlers going west to California.
In 1848 the river was explored by John C. Frémont, who made a thorough map of the region and gave the river its current name. The following year the river became the route of the California Trail, the primary land route for migrants to the California gold fields. In 1869 the river was used as part of the route of the Central Pacific segment of the Transcontinental Railroad.
In the 20th century, the valley of the river became the route for U.S. Highway 40, later replaced by Interstate 80. About 45,000 people live within 10 miles of the river, roughly a third of the population of the state outside of western Nevada and Southern Nevada.