What substrate are you using?  What do you feed your gecko?  If you feed your gecko crickets, it may be pinhead crickets you're seeing.  If you're using a bioactive substrate (like coco fiber) it may be springtails, which are part of the cleanup crew, and they are probably going for the water bowl because the enclosure is probably drier than they prefer. If you're seeing them crawling around at the top of the enclosure where the lid rests, it's probably grain mites (which are not the kind of mites that infest a lizard's body) but that would be unusual unless you have some kind of grain in the enclosure. It's probably not mites that infest a lizard and probably OK for your gecko.
Aliza 
Aliza