I read in several livestock books, whilst researching what animals to have, that you shouldn't give any animals water that's been collected from rooftops (ie, through the guttering). This is because of the risk of contamination from birds perching on whatever structure the water is running off, be that field shelter or house, and pooping all over it. I guess if you can put spikes up on the roof to stop birds perching on it, the rainwater runoff will be absolutely fine.
I can't remember the actual disease that the birds can spread through their faeces, possibly listeriosis? I'm just stabbing in the dark here, so maybe someone else can tell me what it is!