Evidence of human presence in the area as old is as 11,000 years, but the earliest campsite at Red Rock Canyon dates from 8400 years ago. We know the native peoples came here for bison, using the natural features of the land to aid them in their hunt. The rolling eskers provided drive lanes, and cliffs above Blakiston Creek a convenient buffalo jump. They followed the seasons, taking shelter in the temperate valleys over winter and hunting other game in the alpine during the summer months. The abundant fish of the Waterton Lakes gave their diet variety, and they used the mountain passes to travel farther afield.

Oral history of the Kootenay people traces their ancestry to southern Alberta, although by the time Europeans entered the area, they were based in southwestern British Columbia. They continued to access the riches of the plains, crossing the Continental Divide by way of Flathead pass and the South Kootenay Pass, known to the Kootenay as the Buffalo Trail. As horses became a part of the culture, and bands travelled further in their quest for bison, conflict was inevitable between competing nations. The Blackfoot Nation, comprised of Peigan, Blood and Blackfoot tribes, expanded their territory to the west, eventually entering the Kootenay hunting grounds at Waterton Lakes. The Kootenay were no match for the Blackfoot, and ultimately relinquished their rights to the plains and mountain passes. But it was a hollow victory for the Blackfoot. Within a few short years, the bison were gone.

In 1858, Lt. Thomas Blakiston, returning eastward from his first exploration of British Columbia, is on record as the first European to have viewed the Waterton Lakes. Blakiston named the lakes Waterton, after British naturalist Charles Waterton, although the locals continued to call them Kootenay Lakes for many years after.

Other trailblazers on the move at that time were the British and American surveying parties sent out to the Pacific to begin marking the International Boundary which had been established at the 49th parallel by the Oregon Treaty in 1846. The Americans arrived at Waterton Lakes in 1860 - the British, the following year. A joint commission was established to mark the boundary from Lake of the Woods to Waterton. They reached their destination four years later in 1874, but working in the mountains proved so difficult that they managed to erect only two markers in the Waterton area.

The International Boundary Commission was established as a permanent organization in 1925, responsible for maintaining the longest undefended border in the world. Visitors to Upper Waterton Lake often marvel at the line, a 20 foot cleared swath through the forests and across the mountains.

Waterton Lakes National Park in Canada and the United States Glacier National Park united to form the world's first International Peace Park in 1932. The union recognizes that political boundaries notwithstanding, it is one ecosystem, each part dependent on the other for its continued viability. Practically speaking, the park managements co-operate on many issues, from fire control to wildlife monitoring. The animals that inhabit the region hold no allegiance to either park. Park staff and visitors alike have suggested allowing the 19 mile visual divide in the wilderness to re-grow as a true symbol of the ‘long-existing relationship of peace and good will between the people and governments of Canada and the United States.’

On December 6, 1995, Waterton-Glacier International Peace Park was officially designated a UNESCO World Heritage Site, recognising its significance in ecological diversity, and its model of cooperation and good will, not as two separate parks, but as one.