The darker water is a spot where you can use the HM move dive. When you use the move, you will dive under the water and you can float around and go through the seagrass to find different pokemon. These spots also contribute to the storyline, but I'm not going to spoil anything just in case.
In Emerald, Pokemon can be found in Grass, Water, and Caves. There are 385 Pokemon in total.
You can.
Rectha
you can use a water stone on lombre
Kyogre.
Water.
Lombre and etc
yes totaly
I believe that the darker patches are to show better depth.
The best water Pokemon in Pokemon emerald I believe is Kyogre. kyogre is probably the stongest but i prefer a swampert if you don't like legenderies
it is on the ship in the water
abandoned ship