If we're talking "deserts" in the sense that there is a bunch of sand and some dunes, then I'd hazard that the Desert of Maine[0] wins this contest at 600 acres smaller (.16km^2 in total) than the Carcross desert (2.6km^2 in total). [0] https://en.wikipedia.org/wiki/Desert_of_Maine
Unlike the Carcross, this one receives too much rain to be classified as a semi-arid desert.
>The dry climate and strong winds in the 260-hectare area make it feel like a real desert, but the Carcross Desert is actually a series of sand dunes (which technically have too much moisture to be classified as a desert).[0]
[0]https://web.archive.org/web/20090612184355/http://www.canadi...