First the Super Rod must be obtained. Then, face a water body or surf. Next press Start, choose Bag, go to key items choose Super Rod, and choose use. (It could also be registered so instead of having to go through the bag, pressing select can cause it to be used immediately. Finally, if an exclamation mark appears above the character's head, press A. Keep pressing A in time with the exclamation marks until the battle begins. If the pokemon got away, or nothing bit the rod, try again.