Unless the rainwater is allowed to sit and become stagnant, I don't think that it would be an issue. Normally if a dog ingests water that is fouled, it would cause vomiting or diarrhea.
Did this limping, swelling and shaking occur after an injury or just develop over time? You said the dog gained 5lbs since his last visit - when was the last visit? Did the vet do any bloodwork?
Livin in a Newfie Drool Zone