Sorry. I'm a little confused by what you're saying. What makes it so that Water biomes aren't at real locations with water? At home I live near a lake, it's a water biome. I go to a pier on the ocean, it's a water biome. Even my college campus, which is in the middle of Los Angeles, nowhere near large bodies of water, has water spawn points next to its fountains and pools, but nowhere else. And if you go somewhere without water, you don't see any Water-Types. I'm pretty sure that water leads to Water-Types spawning.
What I'm trying to say is each water bodie - river/ocean/lake/resivior have a different set off Pokémon in its spawn list . Yes water will spawn water type Pokémon . But it won't spawn every water type .
Reservoir Pokemon
Common 40% Magikarp 20% Psyduck 15% Electrobuzz
Uncommon 10% Slowpoke 5% Magmar 2.5% Dratini
Very Rare <1% Tentacruel Seaking Polwag Golduck Tentacool Slowbro Horsea Staryu Vaporeon Dragonair Squirtle
Compared to
River Pokemon
Common 50% Magikarp 25% Psyduck 15% Slowpoke
Uncommon 2.5% Dratini
Rare ~1% Krabby Golduck Tentacool
Very Rare <1% Tentacruel Staryu Polywag Goldeen Seaking Slowbro Squirtle Horsea Dragonair
Notice how each list is slightly different . so forth with oceans/beaches etc .
So again not all water features are "biomes". Yes they will spawn water Pokémon from a random common list , but tracking down certain "biomes" will increase your chance to find more of the Pokémon you want .
I can walk my river trail and snag water pokes , and maybe get a random totodile , but I know if I head to the pier front I have a higher chance for totodile spawning multiple . Which is a water biome in my area . Not just a water spawn feature like the river walk to the ocean .
Again I'm only going off my finds , I'm over 1500km walked in game , level 31 . Have 122 totodile candie at the moment from hunting in this biome against random water spawns . I've had croconaw and totodile spawn together , or multiple totodile spawns in this small area only . Everywhere else has been a single totodile and hardly repeats the spawn again . Same with dratini I know I can go this point and always get a couple on a days hunt from it, where the river etc may only give me 1 every few days .
You may be lucky and have water biomes in all your water features , but that's not to say it's a biome that has totodile in its spawn listings .
Most biomes have about 5-10% chance to pull any random spawn from the hole Dex available as well as a set list of Pokémon .