It's not typically reccomended to use roofing EPDM in ponds, roofing EPDM often has additives and chemicals that are harmful for both aquatic life and water quality alike. Roofing EPDM often has fungicides and other chemicals that can be incredibly harmful to any fish living in the water. EPDM manufactured for use in ponds is specifically designed so that it is safe for fish and other aquatic animals.
Make sure that you're choosing a specifically designed pond liner that is safe for aquatic life and has been tested for durability and performance in ponds. These liners are usually made from virgin EPDM that is free of harmful chemicals and additives. This will protect your water quality, and any plants or fish you choose to add to the pond.