During the winter at Fort Clatsop, members of the expedition decided to set up an evaporator for procuring salt from the Pacific Ocean's salty water. After boiling the water in cauldrons, men would scrape up the salt left behind. This provided the expedition's men with one of very few luxuries during the winter. Native Americans from nearby tribes were so interested in the salt evaporation that they often came to watch the process. Through one of these curious observers, Sacajawea learned that a huge whale had been beached nearby. Making one of her few personal requests of the trip, Sacajawea begged to go see the whale. Clark, who was fairly bored at Clatsop, agreed to go with Sacajawea and Charbonneau to see the whale. Disappointingly, the whale had already been nearly reduced to a gigantic skeleton by the local Native Americans, who used all parts of the whale for food and oil.

Food was extremely hard to come by during the winter. Sacajawea endeared herself to Clark when she gave him a piece of bread she secretly had been saving for Jean Baptiste ("Pomp"). When they ran out of tobacco, many of the men resorted to chewing tree bark. The expedition was surviving on very little, and ran almost entirely out of items to trade with the local Native Americans. It was truly a desperate time for the expedition.

Despite their dire straits, the expedition never killed any seals for food, although they were happy to accept seal meat the locals brought them. Perhaps Lewis and Clark, unused to this source of meat, never thought of sending men out to hunt seals. According to a Shoshoni legend, Sacajawea mistook the seals for a tribe of aquatic people and tried in vain to talk with them.

Meanwhile, Lewis and Clark had their fingers crossed that Jefferson had sent a ship to pick them up. Although they had left a few of the tributaries of the Missouri River unexplored, at this point they just wanted to make it back east alive, with their journals and specimens intact. Jefferson had not in fact sent a ship; and although an American ship called the Lydia was sailing in the region, the expedition narrowly missed it. As a result, the captains and their men had to return east by the long and dangerous route they had come. On March 22, 1806, Lewis and Clark decided that winter had lifted to the point where they could leave. Turning Fort Clatsop over to the Natives, the expedition began its long journey home. Sacajawea remained with the expedition. With a long journey ahead (they would be fighting against the current of the Colombia River this time), Lewis traded his finest clothes to some locals for another dugout canoe.

Winter at Fort Clatsop, located in modern-day Oregon, represented one of the most difficult stages in the Lewis and Clark Expedition. Clark, usually upbeat, could only describe the situation as "dreadful." Thankfully, the winter proved a mild one by Oregon standards. If it had been a harsh winter, the expedition might never have survived. The group was exhausted, sick, and had very few supplies left. Even Clark's robust servant York--who was otherwise only rarely sick--became gravely ill. The fact that Clark carefully noted Sacajawea's gift of a piece of bread to him shows just how close to starvation the mission had come.

Boredom also plagued the fort, and this restlessness led Sacajawea, Clark, and Charbonneau to go search for the beached whale. Clark also was hoping to bring back some blubber, and the group did return with about 300 pounds of whale fat to add to the Clatsop supplies. In reaching Tillamook Head, where the whale was beached, the trio went as far south on the Pacific Coast as anyone in the Lewis and Clark Expedition ever went. While Sacajawea and her friends were looking for a beached whale, the other men back at the fort were considering another way to alleviate their boredom: Indian girls increasingly tried to prostitute themselves in exchange for the expedition's goods, and despite Lewis and Clark's warnings to their men of the dangers of venereal diseases, many men engaged in liaisons with their visitors. Sacajawea was not the target of advances by men throughout the expedition because her husband was present and, moreover, she carried an infant child with her at all times. Thus the men treated her only with brotherly fondness. They also directed a fondness toward Jean Baptiste during that winter, constantly playing with him and entertaining him. Those who could write did so during the long winter days inside, and as a result the Native Americans around Fort Clatsop became the best documented and most carefully described of the entire expedition. Clark produced meticulous maps of the region while Lewis wrote voluminously on the botany and biology of the Pacific Northwest.

Many members of the expedition pinned their hopes on finding a ship to take them back east. When no ship came along, many men began to panic. This period of the journey proved the most tense of any.