Roofing EPDM is manufactured using a different process than fish and plant safe pond liners. A longer curing time allows EPDM products intended for use in ponds to pass EPA and ASTM fish friendly tests. Roofing EPDM is not designed for ponds and product warranties will not cover fish kills.
Some EPDM roofing material may be treated with a number of chemicals such as algaecides, fungicides, and flame retardant coatings. Since it's not possible to determine what additives or coatings may be included in any particular EPDM roofing product, it's best to stick with products certified as fish and plant safe according to ASTM standards.