Dark Spots on Roof

James, your assumption about the staining below the downspouts is correct—some of that discoloration is runoff carrying dirt, roof granules, and organic debris from the upper roof and gutters. When gutters aren’t regularly cleaned, that dirty water concentrates at discharge points and leaves dark streaks on shingles and siding below.

What’s more telling, though, is the staining you’re seeing where there is no downspout, like the area you marked in red. That points to a different mechanism. In those locations, the staining is most commonly caused by water shedding and slow drainage along the roof surface, not gutter overflow. When rainwater moves slowly across asphalt shingles—especially on shaded elevations—it can carry asphalt oils, fine granules, and airborne contaminants. As the surface stays damp longer, those materials deposit and create dark streaking, sometimes within hours after rainfall.

Other contributing factors I see in situations like this include:

The good news is this is usually a cosmetic issue, not a leak or structural problem. Cleaning the upper gutters will help reduce staining at the downspouts, but it won’t completely eliminate staining caused by natural runoff patterns on the roof itself.

Bottom line: the downspout staining is debris-related, but the staining away from the downspouts is typical roof runoff and shingle aging behavior. If it bothers you visually, a professional roof cleaning using manufacturer-approved methods can improve appearance—but it’s not an urgent repair issue.