Deck stain differs from paint in a major way: Stain soaks into bare wood's pores to become part of the top layers of wood, while paint simply sits on top of the wood. Because it becomes a part of the wood, stain lasts for a long time if you apply it properly. This means applying the stain on a day when rain is not forecast for at least 48 hours. Rain on a newly stained deck can ruin it.
Stain needs to dry for several hours for it to set. Even after that, it needs to remain undisturbed for several days before you put outdoor furniture back on the deck. If it rains within 48 hours after you apply the stain, the water will soak into the wood pores and try to displace the stain. This will result in a splotchy surface rather than an even tone. If it rains right after you apply the stain, the stain will peel and flake off. If your stain has been drying for close to 48 hours, this may not happen.
Stain penetrates wood best when the wood is cool and dry. Thus it is best to apply stain when it is overcast but not rainy. If you have to apply deck stain, do it after the sun has passed over your deck and is no longer directly beating on it. Feel the deck slats to determine if they are still hot, and wait for them to cool if they are.
Wait to stain the deck until the weather forecast indicates that it will not rain for at least 48 hours. For some regions, this could mean waiting several months until you can stain the deck. It might be difficult to wait to stain the deck, but it will prevent hours of extra work.
Fixing Blotchy Stains
If the stain is peeling or flaking off because of rain, you will have to sand the deck to remove the peeling stain and begin the entire process again. If the damage is merely cosmetic and the deck stain feel and looks good except for a few splotches, you can apply stain to the areas that are lighter to attempt to blend them in with the rest of the deck. Wait for the deck to dry completely and the forecast to indicate no rain before refinishing or touching up the stain on the deck.