Petunias do that when they get heavily rained on. Also, they are probably very crowded which encourages mold and bugs. I would cut the stems all the way back to where the new side shoots are starting. Or, just do this to half the stems and deadhead the rest (pick off all the dead flowers with their individual stems-petioles) so you still have blooms. New flowers will appear as fresh as can be.

It's the time of year to cut petunias way back anyway, to encourage branching but more importantly to get blooms on the new growth. Too much fertilizer, though, can cause a lot of pretty leaves and not many flowers.

If wave petunias are still looking very healthy do I wait to prune, or should it be done now regardless.

Petunias are indeed heavy feeders, especially if you have them growing in pots and containers in which they should be fertilized regularly throughout the growing season. It depends what ratio of fertilizer you are using, look for a higher middle number such as Miracle Gro 15-30-15 or better yet 10-52-10.

Regardless if they look healthy, I would start pinching or cutting back every other stem every other day, this will generate new growth and more blooms all season long.

Sharon