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I just started on Pokémon Pearl and I wanted to use a Ground/Water type for my team. I know there are two Pokémon lines with these types, the Wooper line and East and West sea Gastrodon. But I’m not sure which one to choose. Should I use one of these or should I stick with my starter, Piplup/Empoleon? (Moveset too please ;-;)

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I think Empoleon and Gyarados are better than both Gastrodon and Quagsire, mostly because they have higher attack stats.
Why do you want to use Quagsire/Gastrodon with the Piplup line?
Piplup because I chose it as my starter, and Quagsire/Gastrodon because they can learn Ice-type moves for Cynthia’s Garchomp. (I think Gastrodon can) And their Ground-type attacks are Super-Effective against her Lucario too.
Empoleon can learn Ice-type moves too.
I know, and true it’s special attack is higher than both of them, but it has more weaknesses. I want a team of various types, with as little weaknesses as possible.
In general, Pokemon with higher attack stats or more powerful moves are better than Pokemon with less weaknesses. Offensive Pokemon can win battles faster and spend less time dealing with stuff like confusion or evasion boosts. If you don't care about your time, you can just pick 6 random Pokemon, raise them to level 100, and win the game that way.

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In general, Pokemon with higher attack stats or more powerful moves are better than Pokemon with less weaknesses. Offensive Pokemon can win battles faster and spend less time dealing with stuff like confusion or evasion boosts. If you don't care about your time, you can just pick 6 random Pokemon, raise them to level 100, and win the game that way.

Another thing is that it's often not a good idea to overprepare for one Pokemon, like Cynthia's Garchomp. Yes, Cynthia is a difficult battle, but so are Wake, Candice, Cyrus, Lucian, and several other opponents. Preparing for one will hinder you against the others, and using a generally good team means generally doing well.

In Pearl, the water Pokemon with the best attack stats (and are also obtainable pretty early) are Empoleon and Gyarados. These are the movesets that I recommend. If you choose to go with Gyarados, you might want to catch a level 19 (or higher) Magikarp after getting the good rod, so it starts at a higher level and evolves faster.

Empoleon @ choice specs
EVs: 100 Spe
- surf
- flash cannon
- grass knot/hydro pump
- ice beam

Gyarados @ mystic water/splash plate/expert belt
EVs: 100 Atk
- waterfall
- dragon dance
- ice fang
- return/earthquake/stone edge

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I may sound dumb for this, but where can I find the Good Rod?
You can get it by talking to a fisherman on the south side of Route 209.
source: https://bulbapedia.bulbagarden.net/wiki/Good_Rod
Okay, thank you!
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Due to the fact Empoleon is a specially oriented attacker/defensive Pokémon, I suggest either going with Quagsire or opting for Gyarados. If you need something to deal with Garchomp, Gyarados is immune to earthquake and can also set up dragon dance.

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But why would anyone want 2 water Pokemon on the same team?