Lewis and Clark spent a month scouting possible locations for their winter quarters once they realized that there were no sailing ships along the coast that could take them home.  The Corps selected a site on high ground within a thick grove of towering trees two miles up the Netul River and south of the Columbia River's mouth.  Work on log cabins and fortifications began on 9 December and was not completed until the end of the month.  Fort Clatsop was named for the closest tribe of Indians – the "La t cap" (meaning "place of dried salmon") – whose nearest village was seven miles away.

The Clatsop were a small Chinook-speaking tribe of some 200 people living in three separate villages of large cedar-plank houses.  Although many Clatsop visited the American fort and were friendly enough, trading, not socializing, was their main reason for coming.  Only Coboway and Cuscalar, two Clatsop headmen, appear with any regularity in Lewis and Clark's journals.

To the south of the Clatsop, about 30 miles from the American fort, lived the Tillamook tribe of 1,000 people.  They were Salish Indians who also spoke some Chinookan terms useful in trade.  The largest and most important of the Chinook villages were located many miles from Fort Clatsop on the north side of the Columbia River near Bakers Bay.  Chinook chiefs Comcomly, Chillarlarwil, and Taucum, accompanied by warriors well-armed with muskets, paid official visits to Fort Clatsop.  They smoked with Lewis and Clark and received peace medals and other gifts, but the explorers never visited their villages.  It almost seemed as if Lewis and Clark gave up on the idea of a U.S. trade alliance with the coastal tribes because those Indians were already so attached to British business interests.

The Americans were also tired and miserable during the long winter at Fort Clatsop, eager to return home and devoting most of their time to finding food and firewood.  While the Corps of Discovery seemed to enjoy their first winter among the Mandan, they merely endured the winter near the Clatsop.  Along the Oregon coast, the Americans did not have to worry about freezing to death, but the bitter cold and deep snow of the northern plains were replaced by constant drizzle, fog, dangerous thunderstorms, hunger and poor food, rotting clothes, and stinking, wet cabins filled with fleas and slugs. 

Hunting elk, killing and cooking dogs, tanning animal skins for both wearing and trading, and making 358 pairs of moccasins were other ways that the Corpsmen occupied themselves.  Lewis and Clark spent their time writing reports, drawing maps, and compiling detailed information on Indian cultures and populations. They estimated that there were 80,000 living west of the Rocky Mountains in 1806!

Unlike the winter at Fort Mandan, the explorers rarely enjoyed festive entertainments with the local tribes.  Corpsmen celebrated Christmas and New Year's Day alone, and they only opened Fort Clatsop to Indian traders 24 days in a four-month period   The Americans had to be more self-sufficient in obtaining food and other supplies because the Chinookans charged too much for their products, and the Expedition's supply of "Indian presents" brought from St. Louis was almost all gone. (The Clatsop did make Lewis and Clark custom-fitted woven rain hats.)  

Contact with Indians was also limited because so many American possessions were stolen.  Corpsmen were on guard all of the time and refused to allow even Indian chiefs to stay overnight in the fort.  Theft so frustrated and angered Expedition members that "No Chinook" became the required pass for gaining entry into Fort Clatsop!