Commercially available side-scanning sonar units sold for anglers are a good, low-cost option for substrate classification in rivers and lakes. The units are small, portable, and very inexpensive. Unfortunately retrieving data from these units often involves replaying data on the unit itself or capturing screen shots which are typically distorted representations of the bottom. Overlaying the data on a map could be very helpful. I put together a quick C++ project to turn Humminbird 698ci side images into georeferenced TIFF files for a river surveying project. The focus is on legibility and some spatial accuracy is sacrificed for image clarity. The project as well as a fuller writeup of how to use it can be found on github here: sonar gridder.
Check out my other projects on github too while you are at it!