Hi cadams87,
Amphibians are even more sensitive to water than most fish because they breathe through their skin as well as their gills. You are about to spray a pesticide - a chemical deadly to certain life forms. You definitely need to cover your tanks.
The fogger (I am assuming that is what you mean?) will have directions on how long to leave them alone before re-entering the room, right? You should cover the tanks for at least that long, maybe an additional hour or two just to be sure. It is not enough just to lay something over the tank; you should also seal it (duct tape to the rescue!
).
The best thing I can think of would be to move the entire aquarium somewhere else for the fleas treatment. Barring that, I image I would try to make a cover out of something that extends beyond the perimeter of the tank. A blanket or towel or something would not be enough cover; I should think something more like plywood would be better?
I am also wondering about the filter - if you have an external filter, they have air slits in the sides. I am not sure, but I suspect that might pose a problem, too?
Maybe a tarp laid over the entire system and then taped to the floor?
The only other suggestion I have would be to use something other than a fogger - like a floor mop pesticide or something. I can't see where you are from (nationality) so I can't begin to guess what products are available.
Please do update on what you decide.
-Eva