It's a metaphor, and it compares the mind to a fountain, like you might see in a park. If the fountain is "stirred" - i.e. swished around, or moved - the mud at the bottom of it clouds the water, preventing you from seeing the bottom of the fountain.
And therefore, the human mind, when stirred up with thoughts swirling around, becomes clouded: and, to use another metaphor, it's very difficult to get to the bottom of things. As with the fountain, a confused mind makes it difficult to see things clearly.
Hope this helps!