Lee served a second tour of the Philippines as G-2 of the Philippine Department from September 1923 to July 1926. On returning to the United States, he was posted to Vicksburg, Mississippi, as the District Engineer. This coincided with the Great Mississippi Flood of 1927, the most destructive river flood in the history of the United States. Over were flooded, 162,000 homes were damaged and 9,000 homes destroyed. Lee directed relief work, attempts to shore up the levees, and evacuations of towns and districts. The United States Congress responded with the Flood Control Act of 1928, which provided for improved flood control measures. Lee supervised works on the Red River, Ouachita River and Yazoo River. The legislation moved the headquarters of the Mississippi River Commission from St Louis to Vicksburg, where it was located at the center of the flood area but well above the level of the river. Lee directed the construction of the new headquarters facility, and of the Waterways Experiment Station there.