If the water was an amber yellow, it is most likely just tannic acid from the decaying wood and bark in the potting compost. If it was bright chrome yellow, a dye is possible, though that tactic is rarely used in Begonias, and is usually visible in the leaf veins, as well as the flowers. What kind of Begonia is it, Barbarak? There are several types that are sold as houseplants, and one of them has naturally yellow flowers.

I know with colored moth orchids, the dye must be injected into the stem for each flowering cycle. If not, the orchid will be white - its natural color. As Tug stated, I think you have a yellow begonia. It's probably just planted in some decorative colored compost.