Not only is this a good resource for boating the San Juan, it's a great guidebook about the areas history, geography and biology. It goes above and beyond what your typical mile by mile guides do. The only thing preventing me from giving this 5 stars is that it lacks campsite descriptions.
The San Juan River Guide, by Lisa Kearsley, explores 83 miles of the San Juan River in southeast Utah. This waterproof guide covers everything from the geology and biology of the area, to the river itself.
This guidebook is interesting, comprehensive, and well-illustrated. It gives you a feel for the river and its surrounding environment - from archeological sites to the plants and animals - as well as its history, logistics, safety, and the threats facing the San Juan River. The guidebook includes a detailed river map section.