Just put a permanent, impenetrable dam between Lake Michigan and the Chicago river - the watersheds return to the condition they were before people meddled with the geography of the watersheds. Problem solved.

There's no good reason for any connection between the Great Lakes and the Mississippi watershed; the only reason there's one now is so plains and southern states can divert Great Lakes water for their own purposes, such as raising the level of the Mississippi river during drought conditions, etc. Screw 'em - if the river's low they need to learn to deal with it.