The expedition was in the area of the Missouri River in Montana where the Marias River enters into the Missouri from the north. The confluence of the Marias and Missouri rivers is about 1 mile south of Loma, Montana.
They weren't sure which river was the Missouri so Lewis headed north up the Marias River and Clark headed up the Missouri which leads to the Great Falls, then to what is present day Helena, Montana, and eventually to the Three Forks of the Missouri made up of the Madison, Gallatin and Jefferson rivers.
The expedition would leave the Marias river on June 12 and take until July 15 to cover only 100 miles upstream on the Missouri, due to the difficult portage.
Lewis's portable iron-frame boat sank during this time. This boat has an interesting place in the expedition. Lewis had delayed starting the trip from St Louis for some time waiting for this special boat to be finished. It was made of strap iron, could be disassembled and carried upriver until the party reached a point where the larger boats were no longer practical. Because of the difficult and long portage, the Great Falls of the Missouri were the perfect place for the iron-frame boat to be put together and used. It was to be covered with animal hides, which was not a problem since there were many buffalo in the area. The hides were to be sealed with pine pitch, unfortunately there were no pine trees in the area and the improvised ground charcoal and tallow sealing compound did not work and Lewis's boat sank, which forced the expedition to spend 5 days hewing boats from the cottonwood trees near the river.
Sacajawea had become ill with a fever and Lewis was treating her with some frontier medicine.
A simple Google search for "Lewis and Clark" returns a wealth of material.
A great book about the expedition is "Undaunted Courage
Meriwether Lewis Thomas Jefferson and the Opening of the American West" by Stephen Ambrose.
