On January 11, 1993, the Motor Boat Cruise closed permanently, in part due to the negative reactions to the Gummi Bears overlay, as well as its operating budget being needed for Mickey's Toontown.
In 2001, an attraction considered by WDI to be the true successor to the Motor Boat Cruise, Aquatopia, opened at Tokyo DisneySea in Japan.
In 2007, the former Motor Boat Cruise waterways were drained during construction of the neighboring attraction, Finding Nemo Submarine Voyage.
In April 2007, a new dam was built, and water filled back into the area known as Fantasia Gardens (the former Motor Boat Cruise loading dock).
The Motor Boat Cruise's old dock was repurposed into a waterside dining area for the neighboring Edelweiss Snacks, and is used as one of many locations to hand out candy during Mickey's Halloween Party.