
To avoid excess algae, put your waterer out of the sunlight and evaluate the condition of your water. Adding a little vinegar to the water to acidify it can discourage algae growth, but won't help much if your chickens' water gets droppings scratched into it (adding "fertilizer") or if your waterer gets a lot of sun. You also won't want to add vinegar if your waterer is the galvanized metal variety, as that could encourage early rusting.
A last idea would be to switch to a smaller waterer that gets filled and cleaned more frequently, and so doesn't sit around long enough for algae to grow.