My bike got caught in the rain, and 12 hours after being covered, the seat it still wet. What's the best way to waterproof a bike seat, so I don't have to worry about having a big wet spot on the back of my pants when I get to work?

You don't say what the saddle material is but you normally want it to breathe. Best thing us just leave it alone.

Back in my diamond frame riding days I stuffed a plastic grocery bag from the supermarket under my saddle. Whenever I parked my bike when I thought it might rain, I tied that bag over my saddle. Good enough and the price was right. Doesn't work with a recumbent seat.

Buy a Pleather topped saddle , the plastic will wipe dry.. PDW saddle is made in a foam that has the molded skin,
smooth and is non absorbant. even if the skin gets scuffed..

https://www.ridepdw.com/goods/cockpi...hronous-saddle

What is your saddle made out of? If pleather, you may have a cut in it.

Is it one of those squishy saddles with foam of some sort inside ? They may hold moisture for a while.

It's one of those lycra lined gel saddles by Serfas. I found a waterproof seat cover by the same company that fits the saddle perfectly. I left my bike inside and it was still wet the next day and left my backside a bit wet the next day. Hopefully the new cover does the trick.

In a pinch you can just put a plastic Walmart or other kind of plastic bag on the saddle and ride. The bag will keep the water off your shorts, you won't notice any difference in comfort.

Put a shower cap on the saddle when it starts to rain.

Yeah, I was thinking of stuffing a bag underneath the seat, or maybe even a shower cap, for some added protection.

I also use a grocery bag.
That way, I'm recycling while cycling!

+1 for plastic bag. If I forget to put one and my seat is wet in the morning, then I just put the bag on top and ride while sitting on it, then remove when reaching destination.