What were Thomas Jefferson's goals for the expedition?

Answer 1

First of all, it was Meriwether Lewis who was assigned to explore the West. Clark would offer to join up with the Discovery Corp weeks after Meriwether Lewis started his journey in Pittsburgh (yes, that's right, Pittsburgh, not St. Louis. Check out the related link to the Lewis and Clark Journals for that fact)

Jefferson's instruction to Lewis were:

"Beginning at the mouth of the Missouri, you will take observations of latitude and longitude at all remarkable points on the river, & especially at the mouths of rivers, at rapids, at islands & other places & objects distinguished by such natural marks & characters of a durable kind, as that they may with certainty be recognized hereafter....The variations of the compass too, in different places should be noticed."

(considering the Native Americans) "...You will therefore endeavor to make yourself acquainted, as far as diligent pursuit of your journey shall admit with the names of the nations & their numbers, the extent & limits of their possessions; their relations with other tribes or nations; their language, traditions, monuments, their ordinary occupations in agriculture, fishing, hunting, war, arts & the implements for these, their food, clothing, & domestic accommodations, the diseases prevalent among them, & the remedies they use, moral and physical circumstance which distinguish them from the tribes they know, particularities in their laws, customs & dispositions, and articles of commerce they may need or furnish & to what extent."

"Other objects worthy of notice will be the soil & face of the country, it's growth & vegetable productions, especially those not of the US; the animals of the country generally & especially those not known in the US; the remains & accounts of any which may be deemed rare or extinct; the mineral productions of every kind, but more particularly metals, limestone, pit coal & saltpetre, salines & mineral waters, noting the temperature of the last & such circumstances as may indicate their character; volcanic appearances; climate as characterized by the thermometer, by the proportion of rainy, cloudy & clear days, by lightening, hail, snow, ice, by the access & recess of frost, by the winds, prevailing at different seasons & the dates at which particular plants put forth or lose their flower or leaf, times of appearance of particular birds, reptiles or insects."

Answer 2

The main objective of the Corps of Discovery was to explore the Missouri River and look for an easy water route across the continent.

However, President Thomas Jefferson also wanted the Corps of Discovery to explore the Louisiana Purchase to study the area's plants, animal life, and geography and to learn how the Louisiana purchase could be exploited economically by expanding the fur trade.

Jefferson wanted to establish trade with the native peoples along the Missouri River and establish US sovereignty over them.

Jefferson also wanted to document US presence in the Pacific Northwest in order to establish a claim to the area before other Europeans could claim the land.