If you want a really rare and strong water Pokemon than get a "Milotic". Milotic is the evolved form of feebas which is extremely hard to find. It is hard to explain how to get a Milotic but if you search "How to get a Milotic in Ruby/Sapphire/Emerald?" In Google than you should find how to get it.
Groudon is rare and you get him just by following the story line. The only other "rare" Pokemon I'm aware of in Ruby would be Relicanth, a rock/water type fish Pokemon that can be found underwater.
tropius is a rare pokemon. but you can catch him near the water institute.
You can get three rare candies in Pokemon ruby sapphire and emerald
...and?
Solrock is not such a rare Pokemon but you can only get them in ruby/emerald
n e where
You catch them. Or trade for them.
Use dive while surfing and when you find a cave under water enter it and explore the cave and depending on which Pokemon version you have sapphire or ruby depends on which rare Pokemon youll find
Rare Pokemon come randomly when you're in the grass or cave.
Use a super rod in the water near lilycove city its pretty rare though.
use the itemfinder
There are a few rare Pokemon you can get in the safari zone they are pinsir, wobuffet and girafarig.