Thompson declined to run for reelection in 1923 and he was succeeded by William Emmett Dever. Thompson left office as Mayor on April 16, 1923. While out of office, Thompson was appointed chairman of the Illinois Waterways Commission. He used his position to remain relevant in the media, involving himself in civic suits and campaigning for the Lakes-to-Gulf waterway project: to build a waterway from the Great Lakes to the Gulf of Mexico. Promoting both the project and himself, Thompson set off on a "scientific" expedition (to be extensively covered by the media), which he set off to the South Seas in order to find a tree-climbing fish on July 5, 1924. Attracting more attention, Thompson placed a $25,000 bet on his success, but no one participated.