I tried shoe covers and must have a couple of pairs from different manufacturers somewhere around. I found them too cumbersome in practical use, awkward to put on and take off, and awkward to wear, far more bother than gain. I use either a rain cape or parka that both spread out up to handlebars in the rain and protect the shoes enough from above. As to the bottom, I have a generous mud flap on the front wheel and, if I ride rapidly over a puddle, I raise my feet.