Get some polyquat as quickly as you can, and add it. You have no circulation in the water on the cover; it will turn green quickly if you don't treat it. www.poolsolutions.com/polyquat.html

Meanwhile add 1/4 - 1/2 gallon doses of bleach each evening. Or, if you have some dichlor, you can use that. Do NOT use trichlor or cal hypo -- either could burn through the tarp, which usually not very chemical resistant.

By the way, I'd be grateful if you can get a series of pictures of the whole process -- many people have a hard time getting a clear idea of what we mean, when we describe this.