Your questions may also be used on the radio show, Talkin' Pets. I could use a little more information, but I'll give it a shot. There are quite a few factors that can influence the quality and temperature of the water that runs off your roof. The type of roof material could be affecting the ph, lowering it to a point that it's too acidic for the fish. Also, the roof temperature could be causing the water to heat up, affecting the amount of dissolved oxygen in the water.
Airborne pollutants can also land on the roof and end up in the runoff.
As you can see there are many reasons why the could be happening. I suspect that the ph spikes might be the problem. You can monitor the runoff with a simple test kit. There are methods to filter the water if you plan to use it. Dear EE, I live in the southeast of the country and we have had a very cold winter here.