A cover system for a storage pond formed using a liner is disclosed. A cover flap, a liner flap and an anchor flap are preassembled either off-site at a factory or on-site. The anchor flap is disposed in an anchor trench and the anchor trench is backfilled. The liner is deployed and the perimeter is welded to the liner flap. The cover is deployed and the perimeter is welded to the cover flap. The above welding is preferably fusion welding and could take place in any order.