Ok, this is how you deal with bulky waters on a rain team:
Option 1: Zapdos or Raging Bolt
Zapdos is seen on a large amount of Rain teams due to its ability to spam both STABs, Thunder and Hurricane, with 100% accuracy. Most Zapdos on Rain teams opt to use a Z crystal like Flynium Z to alleviate the fact that Hurricane is not 100% accurate outside of Rain, which, coupled with Flying's great offensive coverage in the metagame, can smack a lot of Pokemon (and regarding Thunder's accuracy outside of rain, Volt Switch is Zapdos's common last move, so that's still there). Zapdos also gets Roost, which helps it a lot, and Heavy-Duty Boots can alleviate hazard pressure if need be.
Zapdos @ Flyinium Z / Heavy-Duty Boots
Ability: Static
IVs: 0 Atk
EVs: 252 SpA / 4 SpD / 252 Spe
Timid Nature
- Thunder
- Volt Switch
- Hurricane
- Roost
Raging Bolt is rarer due to its lower Speed and worse Dragon STAB, as Draco Meteor lowers your Special Attack and Dragon Pulse is weak af (relatively speaking), and Archaludon already exists as a rain staple Dragon. However, some Archaludon-less teams have made it work. Bolt basically runs the same set as Zapdos: Thunder, the other STAB in Draco Meteor, Volt Switch, and Thunderclap over Roost since Bolt has no healing option. I've seen Dragonium Z quite a bit, although something like Heavy-Duty Boots can be appreciated if the team lacks a good removal option, like Iron Treads.
Raging Bolt @ Dragonium Z / Heavy-Duty Boots
Ability: Protosynthesis
IVs: 20 Atk
EVs: 252 SpA / 4 SpD / 252 Spe
Timid Nature
- Thunder
- Draco Meteor
- Thunderclap
- Volt Switch
Option 2: Archaludon
Archaludon's Electro Shot is so powerful that, in Rain, it's like its third STAB. I don't think I need to explain how this can easily dispatch bulky waters (granted, it does have to be in Rain). You could go with the standard Assault Vest + Stamina set, or (as I've seen a few people run for some reason), Sturdy + Dragonium Z for one of the most nuclear bait mons. I'll just suggest the Assault Vest + Stamina set.
Archaludon @ Assault Vest
Ability: Stamina
IVs: 0 Atk
EVs: 80 HP / 252 SpA / 176 Spe
Modest Nature
- Draco Meteor
- Flash Cannon
- Electro Shot
- Body Press
Option 3: Manaphy
Using Manaphy is not advised, but you very much can if for some reason you can't fit any of the mons above.
The thing with Manaphy is that it gets this neat little move called Tail Glow, boosting its Special Attack to astronomical heights. The other thing with Manaphy is that it learns Psychic for some reason. The other other thing with Manaphy is that it somehow also learns Energy Ball. And another thing: this thing gets Hydration, meaning it just shrugs off all status in Rain.
Manaphy @ Leftovers
Ability: Hydration
IVs: 0 Atk
EVs: 252 SpA / 4 SpD / 252 Spe
Timid Nature
- Tail Glow
- Surf
- Energy Ball
- Psychic
Now I will say that this set is walled by most Dragons, notably Roaring Moon, hence why Manaphy commonly runs Ice Beam over Energy Ball. HOWEVER, if you genuinely cannot slot any of the above three Pokemon (and you can slot a Scarf Tapu Lele and be able to play it really well), this is an option. Alternatively, just have Ice Beam over Energy Ball and try to pressure the Mola with boosted neutral Psychics.
In my opinion, slot in Zapdos and Archaludon somewhere on your team; this will be the most effective on a game-to-game basis in dealing with bulky Waters as well as not being dead weight in other matchups.
Hope this helped!