Toward the end of the last glacial period, Tower Rock became inundated.
The Pinedale Glaciation (an ice sheet formed from glaciers originating in the Rocky Mountains) and the Laurentide Ice Sheet (an ice sheet which covered the Great Plains) blocked the Missouri River, which at that time flowed north into a terminal lake.
As riverwater and glacial meltwater pooled at the base of the glacier, it created Lake Great Falls.
All but 15 feet (4.6 m) of Tower Rock was covered with the lake's waters.

Native Americans were well acquainted with Tower Rock.
The Bitterroot Salish and Lower Kootenay often passed by Tower Rock on their way through the Adel Mountains Volcanic Field to hunting grounds.
The Piegan Blackfeet often wintered near present-day Helena, Montana, and passed through the Adel Mountains Volcanic Field by following the Missouri River.
Wickiup frames were often built in the area and reused as native people moved to their summer hunting grounds and back to their winter camps.
The Piegan Blackfeet considered Tower Rock sacred, and conducted ceremonies there.
Individual Blackfeet also visited the site alone for prayer and meditation.

Tower Rock received its modern name from Meriwether Lewis on July 16, 1805.
Tower Rock marked the boundary where the Lewis and Clark Expedition left the Great Plains and entered the Rocky Mountains.
Having completed the portage around the Great Falls of the Missouri and made enough canoes to carry their baggage, the expedition set out from White Bear Island (a little more than 1.5 miles (2.4 km) south of present-day Great Falls, Montana) on July 15.
Starting near dawn on July 16, Lewis took ailing expedition members Jean Baptiste Lepage and John Potts and set out on foot to explore ahead.
Following an Indian trail, they passed Half-Breed Rapids.
Lewis and his companions then became the first non-natives to see Tower Rock that afternoon.
 Lewis gave the landmark its name in his journal:
at this place there is a large rock of 400 feet high w[h]ich stands immediately in the gap which the missouri makes on it's passage from the mountains; it is insulated from the neighbouring mountains by a handsome little plain which surrounds it[s] base on 3 sides and the Missouri washes it's base on the other, leaving it on the Lard.
as it decends.
this rock I called the tower.
it may be ascended with some difficulty nearly to its summit, and from it there is a most pleasing view of the country we are now about to leave.
from it I saw this evening immence herds of buffaloe in the plains below.

Tower Rock was visited by a member of the expedition again in 1806.
The expedition remained a single party after departing Fort Clatsop on the Pacific Ocean.
Having reached Traveler's Rest (near present-day Lolo, Montana), Lewis and Clark decided to split the expedition in two.
Lewis took nine men and proceeded due east, intending to find the Marias River again.
Clark, meanwhile, proceeded south-southeast toward the headwaters of the Missouri, intending to locate the source of the Yellowstone River and explore it until its confluence with the Missouri.
Lewis' group did not visit Tower Rock.
The main party under Clark followed the Bitterroot River south to Sula, Montana, where it turned south toward Gibbons Pass and the crossing of the Continental Divide.
Following a series of creeks and trails southwestward, Clarks' party reached the Big Hole River, following it to the Jefferson River and then to the Missouri again.
At Three Forks (where the Jefferson, Gallatin, and Madison rivers join to form the Missouri River), on July 13, 1806, Clark ordered Sergeant John Ordway to take a group of nine and go down the Missouri to the camp at White Bear Island and there await Meriwether Lewis.
On the afternoon of July 17, the Ordway party approached Tower Rock.
But high winds came up, causing heavy waves which nearly swamped the canoes.
The Ordway group was forced to spend the afternoon and night near Tower Rock before proceeding past Half-Breed Rapids the next day.
Ordway reached White Bear Island on July 19.
Toward the end of the last glacial period, Tower Rock became inundated. The Pinedale Glaciation (an ice sheet formed from glaciers originating in the Rocky Mountains) and the Laurentide Ice Sheet (an ice sheet which covered the Great Plains) blocked the Missouri River, which at that time flowed north into a terminal lake. As riverwater and glacial meltwater pooled at the base of the glacier, it created Lake Great Falls. All but 15 feet (4.6 m) of Tower Rock was covered with the lake's waters.
Native Americans were well acquainted with Tower Rock. The Bitterroot Salish and Lower Kootenay often passed by Tower Rock on their way through the Adel Mountains Volcanic Field to hunting grounds. The Piegan Blackfeet often wintered near present-day Helena, Montana, and passed through the Adel Mountains Volcanic Field by following the Missouri River. Wickiup frames were often built in the area and reused as native people moved to their summer hunting grounds and back to their winter camps. The Piegan Blackfeet considered Tower Rock sacred, and conducted ceremonies there. Individual Blackfeet also visited the site alone for prayer and meditation.
Tower Rock received its modern name from Meriwether Lewis on July 16, 1805. Tower Rock marked the boundary where the Lewis and Clark Expedition left the Great Plains and entered the Rocky Mountains. Having completed the portage around the Great Falls of the Missouri and made enough canoes to carry their baggage, the expedition set out from White Bear Island (a little more than 1.5 miles (2.4 km) south of present-day Great Falls, Montana) on July 15. Starting near dawn on July 16, Lewis took ailing expedition members Jean Baptiste Lepage and John Potts and set out on foot to explore ahead. Following an Indian trail, they passed Half-Breed Rapids. Lewis and his companions then became the first non-natives to see Tower Rock that afternoon.  Lewis gave the landmark its name in his journal:
at this place there is a large rock of 400 feet high w[h]ich stands immediately in the gap which the missouri makes on it's passage from the mountains; it is insulated from the neighbouring mountains by a handsome little plain which surrounds it[s] base on 3 sides and the Missouri washes it's base on the other, leaving it on the Lard. as it decends. this rock I called the tower. it may be ascended with some difficulty nearly to its summit, and from it there is a most pleasing view of the country we are now about to leave. from it I saw this evening immence herds of buffaloe in the plains below.
Tower Rock was visited by a member of the expedition again in 1806. The expedition remained a single party after departing Fort Clatsop on the Pacific Ocean. Having reached Traveler's Rest (near present-day Lolo, Montana), Lewis and Clark decided to split the expedition in two. Lewis took nine men and proceeded due east, intending to find the Marias River again. Clark, meanwhile, proceeded south-southeast toward the headwaters of the Missouri, intending to locate the source of the Yellowstone River and explore it until its confluence with the Missouri. Lewis' group did not visit Tower Rock. The main party under Clark followed the Bitterroot River south to Sula, Montana, where it turned south toward Gibbons Pass and the crossing of the Continental Divide. Following a series of creeks and trails southwestward, Clarks' party reached the Big Hole River, following it to the Jefferson River and then to the Missouri again. At Three Forks (where the Jefferson, Gallatin, and Madison rivers join to form the Missouri River), on July 13, 1806, Clark ordered Sergeant John Ordway to take a group of nine and go down the Missouri to the camp at White Bear Island and there await Meriwether Lewis. On the afternoon of July 17, the Ordway party approached Tower Rock. But high winds came up, causing heavy waves which nearly swamped the canoes. The Ordway group was forced to spend the afternoon and night near Tower Rock before proceeding past Half-Breed Rapids the next day. Ordway reached White Bear Island on July 19.
Tower Rock State Park