Are you quarantining your rooster? That would be the first thing to do, any time you bring in new birds they should be quarantined for at least a couple weeks, although some would say 60 days.
Do you have any pictures? Does he have any other symptoms like wheezing or any breathing issues? A lot of times respiratory issues will present with watery, yucky eyes.
I would flush his eyes with Veterycin (you can get this at tractor supply or Amazon) or if you can't get that, you could use simple saline solution. If he doesn't present with any respiratory issues, just keep him separate in a warm area and flush his eyes a couple times a day for a couple days.
If any respiratory issues develop, treat him immediately with Tylan50. You can get this at tractor supply as well. Some people give it orally but I prefer to give it as an injection. If you feel comfortable giving an injection, you will need the smallest syringe they sell, 1cc preferably but usually I can only find 3cc there.
Post some pictures and maybe we can help you with a more definitive diagnosis.