Please, please don't paint the bottom of the boat. It is more likely to flake off into the river. Not only does the bottom scratch rocks, but the bottom plastic is more likely to flex and cause the paint to flake. It flexes when you bump hard things, and when hop in to launch.
Painting plastic kayaks with spray paint was a local fad in the mid-1990s around where I live in Massachusetts. there are old photos at the rafting company I work for showing the paint suspended mid-water in eddies and settling out on gravel bars and small sand beaches on our very popular River. I'm not sure how or if the paint flakes affect fish/wildlife. But it's not appealing on the eye. Trust me the old photos prove it. Makes a beautiful place look trashy. Much worse than those one or two boof/common rub rocks on a popular stretch with a little color.