Fishing is one way to catchPokémon in the water. In fact, some Pokémon can only be caught by using a fishing rod. There are three fishing rods that are given out throughout the course of each game, and each one is given out by a Fishing Brother. The exception is in Black and White, where only the Super Rod is available, and it is obtained from Looker.
In Generation I and II, fishing is simply a matter of standing next to water and using the rod. Sometimes, it will hook a Pokémon, and start a battle. Other times, it will catch nothing. There is a random chance of either happening, so if the rod catches nothing, players can feel free to cast it out again.
Generation III
Starting with Generation III, fishing became more complicated, as the player would have to pay attention and confirm as soon as the rod hooked a Pokémon, or else it would get away. In Pokémon Ruby, Sapphire, and Emerald, this required a series of confirmations to reel in better Pokémon. Generation III also introduced the ability for Trainers to fish off the back of a surfing Pokémon, which may be required to catch Feebas.
Generation IV
Fishing in PokéPark: Fishing Rally DS
In Generation IV, the player would use the rod, and an exclamation mark-like sign would pop up above the player, noting that they should push the A button to start the battle with the Pokémon they've encountered. As with Generation III, the Pokémon will go away if the player takes too long.
Generation V
In Generation V, fishing mechanics are mostly unchanged from Generation IV. However, by fishing in rippling water, different Pokémon can be caught, generally being rare Pokémon or the evolved forms of the Pokémon normally found. As such, this allows certain Pokémon such as Milotic and Poliwrath to be caught in the wild, while normally they would not. Furthermore, the Old and Good Rods are no longer available, making the player have a single rod to fish Pokémon with.
PokéPark: Fishing Rally DS is a game focused on fishing for Pokémon. Points are earned for the size, rarity, and species of the caught Pokémon. Up to five Pokémon can be stored at once, and high scores could be seen at Pokémon Centers, while the game was still available for download.
In the anime
Cilan holding a fishing rod
Numerous episodes of the anime have featured the group fishing.
The Super Rod is the only fishing rod that is obtainable in Pokémon Black and White. The Old and Good Rods, while still existent in the game's programming, cannot be obtained without hacking, and cannot be used; however, oddly enough, they can be held by a Pokémon.