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I too had thought about modifying the river bottom so that it had shiny bits. I'm not a fan of metal shine, but I did find out that, with enough tweaking, I can place a secondary water animation as an overlay to the river bottom. Over half of the animated water I pulled from TL2 is actually footage of the bottom surface of a pool or something, not the top of the water. Combining the two makes a very realistic water. That being said, I don't have anything that works well with a rushing stream, just partially calm waters, like a pool. Not a total loss. Hard to really see the bottom of the river bed when water is foaming by. Just those really shiny rocks should stand out, and that is what I really intend for this particular stream.
As you did, I've also used the black texture to darken the water bottoms. I plan to move that into the river systems when I get the bottom texture and edge textures picked out. Much texture shopping to do! For the shallows and deep water, I used a 0-255 transparent gradient, where the top of the texture strip is 100% transparent, and the bottom is full black. I then applied the texture to any bit of water with a 510cm* deep uvwmap cube, positioning the top of the cube exactly with the top of my water level (gmax modifier instances are a life saver). Anything deeper than 5m needs to have a different overlay, but I haven't gotten to that point yet. Haven't run into any place I need deeper than 5m water.
*Just so everybody knows, the extra 10 cm is for avoidance of the texture edge. If you pain a mesh with the exact dimensions of the mesh, there will be blurring (depending on vid card and texture settings) at the edges of your texture swatch when it gets repeated. In my situation, that would carry the full black bottom to the full-trans top, making a black line around the water edge.