William Clark was taking notes that day and recorded the following words about the river water in his journal: "The water we drink or the Common water of the missourie at this time, contains a half a Comm Wine Glass of ooze or mud to every pint-"
You have to keep in mind that the Missouri River of this period was called affectionately the "Big Muddy". It was a wild river that carried untold amounts of silt, clay, sand, trees, grass and who knows what else. All this foreign material was in the river because it was cutting side channels and the currents contained chutes, eddies, boils, undercuts sandbars and backwaters. And things got even worse when there was a big rain up-river somewhere - perhaps the case when William Clark saw it and made his notes.
Today the river is a quite different - with the channel being maintained for navigation and flood control through a system of dams and reservoirs up the river that provide water for irrigation, recreation and power generation. It can still get turbid, but probably not like Clark described it.
There is actually a plaque marker at this site that was erected in 2004 by Kansas Lewis and Clark Bicentennial Commission and the National Park Service. It's in Atchison, KS at the Riverfront Park Pavilion.