Hello,
I know that it can be difficult keeping water clean in a brooder or other chicken environment. Most people don't understand, however, that you don't have to purchase special water container or nipples for chickens. Long before the invention of these containers chickens did just fine using simple bowls or other water tanks. To solve your problem, you have a couple of options to explore.
Firstly, without purchasing water nipples you might have to wait a few weeks before using an open water source. Young chicks will crowd around the water supply and drown those chicks who are small or that can't get out of the way. This happens far more often than most owners will admit. Secondly, you can't use a water supply which is high up off the ground as the chicks will not be able to reach the elevated water supply. Therefore, you might want to consider the idea of purchasing water nipples. I know that it can sometimes be expensive, however, I recently purchased six off
eBay for $0.99 each (plus free shipping) and ended up receiving twelve from the supplier.
If you don't or can't purchase water nipples then you might want to consider the use of a dog/cat water bowl that circulates water. These water dishes will keep water moving, perfect to keep mosquito larva out of the water, and will filter any bedding while used in the brooder. I must warn, however, that this does have to be changed fairly routinely (every 2-3 days) as it will damage the pump if left unchecked.
The best and cheapest way to keep water clean, while in a brooder, is to place the container on a large brick (1 in high x 6 inch long x 6 inch wide). While using this you will not want to put any bedding on the brick and clear away any bedding directly around the brick. This will help prevent chicks from kicking or scratching bedding into the water dish.
I hope this helps...