Nicole, not sure how it would impact the cover but last year we had 3 sets of fiberglass steps full of water and mosquitos ay our shop - I finally got tired of the squtos and crushed a trichlor tab and put a few small peices in each step - the mosquitos went away. I think the cya helped keep the bugs away for ~ 2 mos (which was how long I waited to repeat the proceedure).
Don't know how practical this would be for you (nor the effect on your cover - if the cover would be damaged by the low pH or concentrated cl, it's not worth it), but thought I'd at least toss it out as an idea. BTW, we are talking about a relatively small amt of water, so whatever you use, you shouldn't need much, and it only has to last a month before the cold gets 'em.