There are a lot of ideas in here for how to design river projects, even if you’re not exactly dealing with a road crossing: Guidelines for the Design of Stream/Road Crossings for the Passage of Aquatic Organisms
Even if you are not going to be installing a culvert, you’ll learn a lot about fish habitat restoration design from this article: Designing Road Culverts for Fish Passage
Pronounced “Fish Crossing”, FishXing Software
This software is intended to assist engineers, hydrologists, and fish biologists in the evaluation and design of culverts for fish passage. It is free and available for download. Version 3 of FishXing is in its final beta form.