Technically it's harmless. If your water contains a lot of phosphate run off or other nutrients and is then exposed to sunlight you can get a green water bloom where microscopic particles of floating algae start to grow. Combined together they give it a green tint. Really this is harmless as is most other forms of mild to moderate algae build up. No one's chickens are going to die from a bit of green algae. Black algae and blue/green "algae" (technically bacteria not plant) can sometimes be toxic but brown and green are perfectly safe and may even make your water healthier depending what they are feeding on. While there are people here who think their waterers should sparkle personally I'd just leave it. Some say your water should be clean enough you would drink out of it but we have been so conditioned to only seeing perfection half the stuff we wouldn't drink wouldn't harm us either. Then there's the fact most animals are more durable towards questionable water and food sources than we are and it's very easy to argue that such a level of cleanliness is unnecessary. You can try some acv and it won't do any harm but I don't think it would solve this situation. If you leave the water sit long enough the algae will use the nutrients up and the green water will go away. Some people age water that way for certain uses such as fish tanks or before drinking well water during certain times of the year. No different leaving it sit in another container to do that than leaving it sit in your waterer to do it. Personally I just think water and food containers should be sanitized every so many weeks and kept clean of waste matter and otherwise I don't worry about them being spotless. I doubt you'll find many reports of chickens dying to water that wasn't fresh poured that morning.
I change my waters everyday - I have found that all my poultry prefer the fresh water and with ducks in with the chickens the water gets dirty daily. As soon as I start the hose everyone is there and drinking so I reckon they must prefer the taste!!
I have heard just puting a little bit of apple cider vinigar in the water about 1or 2 tbs per gallon should help. rinse out the waterer really well everytime you fill it I keep a little scrub brush out by the coop to clean it when I fill it too. But I dont have any green in my waterer any more.
I have the same problum with my chickens and my goose. I had to raise up the water dish onto a shelf where the chickens could hop up and get to it but at the same time the goose could still reach her neck up to get some water but couldnt climb in it lol.