I use water based acrylic paints that are sometimes used for T shirt painting, like Createx. You can find them in hobby supply stores, like Michael's, or online at air brush suppliers. Here's one, but there are lots of others: http://www.coastairbrush.com/categories.asp?cat=11
When heated above a certain temperature, their molecules cross link, and become waterproof.
Unfortunately that temperature (I don't know what it is, but I think it's like the highest setting on a clothes iron) are too high for me to be able to reach with ruining my baits.
I use those paints, use a hair dryer to thoroughly dry multiple thin coats (which avoids trapping moisture under a thick coat that will expand later and ruin the bait's topcoat protection), and then protect my paint with a truly waterproof top coating.
If you do a search here for top coat/topcoat you should find lots to read, but the basic topcoats are waterproof epoxies, UV cured polyester resins, acrylic clear coats, moisture cured urethanes, and clear fingernail polish.
I hope this helps.