Since there are so many types of foul weather gear, it might help to know the type of fabric first. Gore-tex? Nylon? Cotton treated with a waterproof coating?
For Gore-tex or Nylon, do not use chlorine bleach, it will damage the fabric.
Mildew/mold weakens fabrics, so killing it is the first priority. Lysol (the brown, nasty smelling liquid) is excellent for this purpose, but it will not remove the stains. Lysol(tm) is nasty stuff, but very effective. I use it to disinfect most everything on a boat. Follow directions. If you don't rinse the surfaces you clean with dilute Lysol, the antimold and antibacterial qualities will remain for some time on the surface.
One way to remove the stains relatively safely is with non-chlorine bleach (the stuff that's "safe for colors"). You might also try diulte Borax. Whatever you use, you should test the cleaner first on a patch of the fabric. For liquid non-chlorine bleach to remove the stains it needs to be applied to dry fabric. I use a soft toothbrush to gently scrub it in, let sit a few minutes, and rinse. Even gentler is using a terrycloth towel or facecloth to do the scrubbing. If it's going to work it will work immediately, not an hour or more later.
As Richard says, foul weather gear has to be washed carefully after use to remove all salt and dirt, then dried thoroughly, preferably in sunlight. Your wet locker should also be cleaned aggressively frequently. Use Lysol, chlorine bleach, even vinegar, to keep that dark hole clean and free of mold.