The problem just comes with it being a CD player. Most stereos don't have fans or even any real cooling issues, so dust doesn't bother them in the slightest. The problem is the optics and the media of CDs, both of which are very very sinsitive to small particulate coatings (CDs will scratch, lasers will dim) under those conditions.
You can certainly isolate it without resorting to anything nearly as drastic as submerging it in a pool. As was mentioned previously, building a case for it is a perfectly viable option. But, as with any method suggested, there is little you can do to prevent it from being at risk when you change the CD, which is really its most vulnerable time. Which is why I suggested the cheap-as-possible route; use it until it breaks, and don't be suprised when it does. Much less hastle, much less expensive, and much easier to use. Or go with something medialess so that you don't have this issue of a CD player at all.