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I don't think any of Disney's hotels have an indoor pool. You may have to look off-property. However, Disney does heat their pools and you can't beat being on-site.
You might want to look into:
Embassy Suites Lake Buena Vista
Embassy Suites International Drive South
These look like the only hotels in my book that list indoor pools as an amenity. All other resort/hotels only list outdoor pools.
Try Diplomat Resort in Kissimmee on I92 West. Used to be Wilson World. They have a very large indoor pool and jacuzzi area inside atrium. Very nice. Five minutes from main gate to Disney and walking distance to many stores and restaurants, etc.
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