Ford estimates that repairs will cost $267 million.
Dealers are to install the water shields and make repairs, if needed, for free.
Ford's F-Series line remained the top-selling vehicle in the country in 2016. Should a customer be able to open and close the door with these conditions, the door may appear closed, but the latch may not fully engage the door striker with the potential that the door could open while driving, increasing the risk of injury.
Ford said it was not aware of any accidents or injuries related to the problem.
2015-17 F-150, built at Kansas City Assembly Plant, Aug. 11, 2014 to December 30, 2016.
The affected models include some of the model year 2015, 2016 and 2017 F-150's, as well as some 2017 Super Duty pickups.
The F-Series has been the company's best-selling vehicle, and the Super Duty, made exclusively at Kentucky Truck Plant, has helped prop up profits because consumers increasingly are opting for higher-end models of the work truck. Ford said it continues to expect full-year adjusted earnings in the range of $1.65 to $1.85 per share.
Sales jumped 5.2 percent to the tune of 820,799 trucks sold in 2016.