Hard to tell without opening the walls.

If you can send me some images (1) exterior showing the rooms affected (2) experior showing the roof (3) some interior images, I propably can tell what the cause is. Remember, you still have to find the source of the leak.

Best scenario, just the window frame and siding need patching, but I don't think so. More likely, you have a leaky roof, some damages in attic and down the wall, some damage to window frame both levels and insulation.