There are various differences among the underwater routes. What remains the same, however, is that they follow the general path of the deep water above them. Sometimes, there will be seaweed along the path; this is very similar to the tall grass of the surface world, where wild Pokémon appear. This is the only situation in Generation III in which the Dive Ball operates at full effectiveness.
While underwater, players can reach otherwise unreachable areas of the routes they are on, which often hide rare items. In Ruby, Sapphire, and Emerald, it is one of two ways to obtain shards, which can later be exchanged for evolutionary stones, the other being to obtain them from wild Pokémon that are holding them.