When you hear on the news how piles of fish and other marine life wash up on shore during an algae bloom (like the green slush covering the shorelines in China), I have to wonder what an overgrowth of algae in a water dish can do to birds.
 
If you have any food-grade hydrogen peroxide on hand (not the stuff in the brown bottle), you can use this (diluted to 3%) to safely clean the water bottles for your birds.  I use this to keep our outdoor birdbaths clean. Pour it in and let it sit for about 10-15 minutes while it bubbles and lifts away the algae, swirl it around and rinse (won't even need to scrub.)  If you don't have any, you can purchase 35% food-grade hydrogen peroxide at health food stores - (you'll need to dilute it, however, but the bottle should come with directions on how to do this.).