The Trench is drained by four major river basins: the Columbia, Fraser, Peace and Liard. Summit Lake north of Prince George is at the low-elevation continental divide between the Pacific (e.g. Fraser River) and Arctic (e.g., Peace River) drainages, demarking the Northern Rocky Mountain Trench from the Southern Rocky Mountain Trench

Although some of its topography has been carved into glacial valleys, it is primarily a by-product of faulting. The northern portion of the Trench is dominated by strike-slip faulting while the southern part of the Trench was created by normal faults.

The Williston Reservoir in the northern Rocky Mountain Trench is fed by the Finlay, Omineca, Ingenika, Ospika, Parsnip, Manson, Nation and Nabesche Rivers, and by Clearwater Creek, Carbon Creek, and other smaller creeks.  Much of the exploration and survey work since the earliest Hudson's Bay Company expeditions relied heavily on First Nations guides, and the network of ‘native walking trails' throughout the valleys and mountain passes of the northern Rockies. 

European exploration of this area began with Alexander Mackenzie's overland travel up the Peace and Parsnip Rivers en route to the Pacific Ocean in 1793, on behalf of the North West Company. Fellow explorer John Finlay returned four year later to explore the northern tributary to the Peace River, later named the Finlay River. No record remains of the expedition except as reported by Samuel Black, Chief Trader of the Hudson's Bay Company. He ascended to the source of the Finlay River in 1824, noting that "he had studied Finlay's chart" and determined that Finlay had likely only made it as far as the Ingenika River, about 130 km north of the Finlay River's confluence with the PeaceEarly exploration focused primarily on identifying travel and trade routes through the region. The first Canadian Pacific Railroad survey was done in 1871, with the Pine Pass through the Rocky Mountains surveyed by C.P.R. engineer J. Hunter in 1877. 

In the late 1800s and 1900s, exploration included mineral prospecting expeditions (e.g., Edward Ruzicka and company, 1900).

In 1897, as the Yukon Gold rush erupted, Inspector Moodie led a North West Mounted Police patrol to establish a route from Edmonton to the Yukon through the Rocky Mountain Trench.   The BC Department of Lands began surveying in the Rocky Mountain Trench in 1912. Mr. F. C. Swannell was the first surveyor sent to the area.  The sensational Bedeaux Expedition ventured up the Muskwa and Kwadacha Rivers in 1931. The Northwest Company was trading furs with First Nations people and trappers during the early part of the 1800s, and amalgamated with The Hudson's Bay Company in 1821.

Local trading posts with provincial significance include Fort McLeod, the first permanent trading post in British Columbia, designated as a National Historic Site of Canada in 1953 and Fort St. James. Less well know, but vital to trade in our region, are Fort Grahame, Fort Ware, and Finlay Forks.  Movement of supplies to the trading posts was by river freighters and pack trains during the early 1900s. Men like Gus Dalhstrom, Edward Buchanan, and Dick Corless, operated river freighting companies to move supplies to the early settlers, from the 1920s until the construction of the Hart Highway in the 1950s. Construction of the W.A.C. Bennett Dam during the 1960s signalled the end of many of the settlements along the Finlay and Parsnip Rivers, as the Williston Reservoir flooded the valley.  Many mineral prospectors have explored the region since 1861, when gold was discovered on the Parsnip, Finlay, and Peace Rivers.  After the Fraser Canyon (1858) and Cariboo (1862) Gold Rushes, miners began to move north into the Omineca District (north of Mackenzie) in search of riches. In 1871, gold was discovered on Germansen Creek in such quantities that a Gold Commissioner was sent to this area to establish a town "Omineca" on a bench three miles from its mouth on June 6. On July 16, an important gold discovery is made on Manson Creek. Only one year later, very few miners remained in the Germansen area, but the Germansen and Manson Creek communities continue to exist today.

When the Yukon Gold Rush began in 1897 and prospectors surged northward, the federal government commissioned the Northwest Mounted Police to find a passable trail from Edmonton to the Yukon, and to police the route.  The first sawmill north of Prince George was at Fort Graham in the 1920s. The sawmill had a 4 Horsepower motor and a 10 inch Edgar blade.  In the early 1960s, the Forest Service built the road from "the junction" (where Highway 97 meets Highway 39) to Finlay Forks.

The Williston Lake Reservoir was created by the W.A.C Bennett Dam on the Peace River at Portage Mountain, 22 km west of Hudson's Hope, BC. It is one of the world's biggest earth fill dams, standing 183 m (660 ft) high, 800 m wide, and 2 km long. The reservoir covers a total area of 1,761 km2 (251 km long and 155 km at its widest point), making it the largest lake in British Columbia and the seventh largest reservoir (by volume) in the world.  The reservoir flooded the Parsnip, Finlay, and Peace River valleys upstream of the dam when construction was completed in 1968. Several communities in the Rocky Mountain Trench were submerged as the water rose (1968-1971), resulting in forceful displacement and relocation settlements for First Nations and homesteaders that lived in the valley. Clearing land to prepare for the flooding of Williston Reservoir opened the doors for the forest industry, and led to incorporation of Mackenzie as an "instant town" in 1966, to house the growing local workforce.