We've done a few base maps for bottoms of lakes and reservoirs using an EDM, shooting to a man in a float tube, holding a prism and a cloth tape with a weight on the end. The EDM and prism give the location, the tape and weight give the depth, which we subtract from the lake elevation to get bottom elevation. You could try this on your river if your site is small, but the water surface elevation may not be constant if your river site is large or has significant gradient. Also, bottom elevations of rivers are likely to change with river flows.