Well, you said it yourself. The water STAINED the deck. You can't clean it per-say.
My best suggestion would be to give the deck a scrub down with bleach, then use a semi-transparent stain on the whole deck. The deck must be as dry as possible when the stain is applied.
Be careful with the bleach. Wear old ratty clothes and GLOVES. Bleach burns, but you don't know it happened till its too late. Eye protection is smart too.
Check with the pros at the local paint store (sherwin williams, cloverdale, kelly moore, etc.) The experts in the store should be able to give you some good ideas on how to approach this, and you can have a dialogue with them, asking as many questions as you can dream up.
Good luck on your deck, don't cover it like that anymore, k?