I believe that the darker patches are to show better depth.
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In the sea, where the water is darker than the surrounding areas.
If you use dive in dark patches of water then go in the seaweed then you can catch chinchou.
Black spots will appear in water when there is a Pokemon there, the Pokemon will be less common than the others on the route
In Pokemon Black & White or any other Pokemon, you can catch water type Pokemon in the sea or by using a fishing rod.
i would say soulsliver becase on soulsliver you can fly and black you cacth water pokemon but on sliver you can get fire pokemon