No personal experience, but in reading about rainwater collection systems someplace, there was a device of some sort which caught the first X number of gallons of water coming off the roof and diverted it away from the path for drinking water. Then, after the roof had a chance to "rinse", the rest of that rainfall event went into the storage tank intended for drinking.

I think adding an air bubbler would help prevent stagnation and provide some circulation of the tank, and a clean, dark, covered barrel from which you occasionally suctioned out whatever settled on the bottom would inhibt other growth through lack of the amterials necessary to grow.

You might check out rainwatercollection.com. Some good information even if you aren't rich enough to buy a complete set up to produce potable water. Please be careful about standing water with the West Nile heading your way.

Thanks. I was thinking of a fish tank bubbler to keep it moving too.
My son saw those diversion setups in Hawaii made out of bamboo...so much water ran away first and then after that it was collected....
A friend of mine here collected water off of the roof...had a water-tower up high to gravity feed below and he ran the water thru charcoal/sand and other layers...and had to clean it somehow periodically......I'm going to ask him more about it.

Please do make sure there's some kind of filtration system in place. Unfortunately, in our world, bird poop on the roof is the least of your problems. Air polution can make your rain water deadly.