There are 2 ways to get a Water Stone in RSE.
Abandoned Ship
There is a Water Stone in Room 3, which requires Dive (that's the clearest Bulbapedia is gonna get, huh...)
Treasure Hunter
On Route 124, West of Mossdeep City, there's a single house (you can't miss it). Inside, you'll find a guy named the Treasure Hunter, who will trade you an elemental stone for a shard, depending on what color shard you have (Red shard = Fire Stone, Yellow = Thunder Stone, Green = Leaf Stone, Blue = Water Stone). To get a Water Stone, you will need to give a Blue Shard to the Treasure Hunter. There are 3 ways to obtain a Blue Shard.
Near the southwest corner of the route, via surfacing through the southwest-most Dive spot (requires Dive)
Source
In the bare square among the seaweed in the very southwest (hidden)
Source
- Clamperl
In RSE, Clamperl has a 5% chance to hold a Blue Shard.
Water Stone acquisition source