Black spots will appear in water when there is a Pokemon there, the Pokemon will be less common than the others on the route
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in Pokemon diamond it is in were the elitle four thing is outside in the water. and that route after it were shaymin is. but you have to use a rod.
In the wild grass you can find: Lillipup,Patrat,Pidove(i am not sure) and less likely -Purrlion In the water: most likely Basculin
You can get a Seel in Pokemon Pearl by finding it in the water on route 226.
Manta (any thing that has to do with water or the pokemon)
When you are on route one go surf on the water and go around to the next piece of land. You can find them in the grass. FYI they are called Watchogs