These are trail running shoes, not dress shoes that you will wear to the opera or to a job interview with a stuffy firm. They will get dirty on the next run, or the run after that, so there is little need to get them pristine after every run.
Therefore, I suggest waiting until the mud has dried, and then brushing the dried mud off. For seams, and the treads on the soles, use a pair of tweezers, or a small screwdriver, followed by brushing with an old toothbrush. If they still don't look good enough for your taste, take a damp cloth of some roughish material (i.e., a small old towel as opposed to a piece of an old pillowcase) and swab the shoes. This will leave them slightly damp, but far from soaking wet.
If there is no mud, but only dry dirt and other clean organic matter, do the same, but the step of waiting until mud has dried is, of course, not necessary. If you have stepped in feces, then you need to get the worst off with a paper towel, then carefully aim a hose with the "beam" at its narrowest at the spot(s), wipe them as dry as you can, followed by brushing, if necessary.