Native Americans fought knowing they might jeopardize their sovereignty, unique cultures, and ancestral lands if they ended up on the losing side of the Civil War.
The main impact that I can think of with regard to this question is that the Civil War helped to cause conflicts between Indians and the United States. The Civil War, of course, took up a lot of government resources. Because of this, Native Americans in the Midwest weren't paid the way the treaties said they had to be.
