Except for permits issued for the appropriation or use of water for agricultural purposes, the Department shall prescribe a time limit not exceeding 2 years from the grant of a permit, during which construction, reconstruction, or repair shall begin or appropriation or use of water shall be completed. The Department shall prescribe a time limit, not more than 5 years from the grant of any permit, during which construction, reconstruction, or repair of reservoirs, dams, or waterway obstruction shall be completed. The Department may extend a permit-time limit for good cause shown.