From Bulbapedia, the community-driven Pokémon encyclopedia.
Puddles of water can be found throughout Hoenn, Sinnoh, and Unova in Generations III, IV, and V. Previous to Generation V, no wild Pokémon can be found in this terrain. Because of this, 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.
Puddles were introduced in Ruby and Sapphire Versions, 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, and his/her reflection can be seen.
Larger puddles appear on the event-only locations Southern Island and Faraway Island. Latios or Latias, depending on the game played, 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. If Secret Power is used in battle here, it may cause the opponent to fall asleep.
Similar to Generation III, they appear with more prominence in the locations of legendary Pokémon.
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 currently 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.
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.
The most notable place in the Unova Region for finding puddles is Sekka City. Large puddles can be found in the southern part of the town, where wild Pokémon may appear.
The Sekka Wetlands are also covered in large puddles.