From Bulbapedia, the community-driven Pokémon encyclopedia.
Puddles of water can be found throughout Kanto, Johto, Hoenn, Sinnoh, and Unova in Generations III, IV, and V. Prior to Generation V, no wild Pokémon can be found in puddles. Due to this, in Generations III and IV, puddles don't have any real use in the game overworld, and are mainly used for scenery; however, in Generation V, many wild Pokémon may be found in puddles. Puddles are well-known for appearing in the locations of Legendary Pokémon.
Differences between games
Puddles were introduced in Ruby and Sapphire, where some areas, such as Route 120 and Route 121, are affected by the rain. When the player character walks or cycles through these puddles, the sound of splashing water can be heard. A reflection of objects north of each puddle can be seen in them.
Larger puddles appear on the event-only locations Southern Island and Faraway Island. LatiosSE or LatiasRE and Mew can be found in these puddles, awaiting capture.
Puddles are again common in rainy areas, such as Route 215. In Diamond and Pearl, the player can battle various non-player characters while standing in this terrain. Similarly to Generation III, they appear with more prominence in the locations of legendary Pokémon.
In HeartGold and SoulSilver, puddles show up in various places in Kanto and Johto, such as Route 34 in Johto and Routes 24 and 25 in Kanto. They were not present in Generation II and are only used as added scenery.
Strangely-shaped pools of water appear in all three caverns below the three lakes of Sinnoh, where the player first encounters Uxie, Mesprit, and Azelf, known collectively as the lake trio. What the shapes of the puddles mean, if they mean anything at all, is unknown.
Two circular, smaller puddles indicate where the other members of the trio are relative to the cavern, so that the two pools and the lake trio member make up a triangle, confirming each Pokémon's status as members of a group. However, battling Uxie and Azelf is considered battling in a cave rather than a puddle, despite both the player and the Pokémon standing in a puddle.
Stylized puddles also appear on both Fullmoon Island and Newmoon Island, the locations of Cresselia and Darkrai respectively. Cresselia is found at the center of a crescent moon-shaped pool, which is a brilliant, bright blue. Darkrai resides at the center of a dark, circular puddle, reminiscent of the new moon. However, battling Darkrai is considered battling in tall grass, despite both the player and Darkrai standing in a puddle.
Puddles are found in the Unova region in Icirrus City, Mistralton City, Moor of Icirrus, and Routes 8 and 9. Large puddles can be found in the southern part of Icirrus City, where wild Pokémon may appear. In winter, the puddles freeze over and wild Pokémon cannot be encountered in them; instead, they act as ice tiles and cause the player to slide over them. Several ponds are in the middle of puddles.
Pokémon Black and White
Pokémon Black 2 and White 2
Certain moves have special effects when used in a battle on a puddle tile. In Generation III, the terrain in battle ignores puddles, so they have no effect.