Answer: OMANYTE
Explanation: The shape of the DNA molecule is a double helix, and the Omanyte fossil is called the Helix Fossil.
Answer: QUAGSIRE
Explanation: Quagsire loves to run away from you in G/S/C, in which it is the only fully-evolved Water-type completely immune to Electric.
Answer: FERALIGATR
Explanation: Yes, extremely obscure clue - the hyphen is a minus sign, and it is referring to how Feraligatr's name lacks one L and one O from the source word 'alligator'.
Answer: POLIWHIRL
Explanation: It is said that Poliwhirl is one of Satoshi Tajiri's favorite Pokémon (him being, of course, the creator of the franchise).
Answer: TEAMROCKET
Explanation: Team Rocket were cutting off Slowpoke tails for selling them in Slowpoke Well in G/S/C.
Answer: STARPIECE
Explanation: Wild Staryu may hold Stardust or a Star Piece, of which the Star Piece is the rarer and more expensive one. Some fans have joked about Stardust being a Pokémon world drug. (The Cave of Dragonflies does not endorse the use of drugs. They mess up neurotransmitters in your brain, you know.)
Answer: RAINDANCE
Explanation: Hey, why would any responsible Pokémon mother let their youngsters use Swords Dance? At least water doesn't slice anybody up.
Answer: QWILFISH
Explanation: Cyndaquil and Quilava have 'quil' in their names, but Qwilfish's name has a W (contrary to how a Q is ordinarily always followed by a U in English words), making it evident that they are not related - not that it wasn't fairly evident already.
Answer: GOLDUCK
Explanation: Golduck has 'duck' in its name, but is commonly thought to be based on a platypus, and sometimes even on a kappa monster from Japanese mythology.
Answer: SEEL
Explanation: Seel always has its tongue stuck out, and living in cold environments like the Seafoam Islands, one has got to wonder...
Answer: LUDICOLO
Explanation: Ludicolo's Japanese name is Runpapa. Split it into two words and you'll see what I meant by the clue.
Answer: REDSHARD
Explanation: 20 down is Corsola, which may hold a Red Shard in the wild.
Answer: ANORITH
Explanation: 13 down is Water Gun, and Anorith learns it naturally. 'First' actually refers to being the first one in the alphabet - the others are Azurill and Castform.
Answer: MIRORB
Explanation: 23 across is Ludicolo, 22 down is Lombre and 17 across is Rain Dance, all of which Miror B. likes to use. For the disco part, I think we all know the connection there.
Answer: MARSHTOMP
Explanation: Marshtomp is most likely derived from 'Marsh' and 'Stomp', meaning there is an extra H in 'Stomp'. And eh... try for yourself to replace it with a 'Hi'.
Answer: HORSEA
Explanation: There is a trick on Pokémon Stadium where nicknaming Pokémon certain things will cause them to be colored differently in the game. Most of the time the key nicknames reverse the first and second halves of the name (for example, Pinsir's secret name is SIRPIN). Horsea's name itself is created from doing a similar thing with the word 'seahorse'.
Answer: POLITOED
Explanation: Poliwhirl (11 across) evolves into Politoed when traded with a King's Rock.
Answer: HYDROPUMP
Explanation: Hydro Pump used to be pretty much Blastoise's signature move if anything was; it was what it was blasting out of those cannons, at least. However, now with the dawn of Hydro Cannon, Hydro Pump is just an ordinary, common best-move-of-type.
Answer: GROVYLE
Explanation: A true Water lover probably starts with Mudkip in R/S/E, in which case his/her rival will pick Treecko. As the rival's starter never evolves to its final form in R/S/E, you'll never see Brendan or May with a Sceptile - the last time you battle, your rival will have a Grovyle as their last Pokémon.
Answer: SEAINCENSE
Explanation: The 'place of the dead' is Mount Pyre, where the Lax and Sea Incenses can be found. They are the items that need to be attached to Wobbuffet and Marill to make their eggs hatch into Wynaut and Azurill - it's the Sea Incense rather than the Lax Incense because this is after all a Water-themed crossword.
Answer: AZUMARILL
Explanation: Azumarill is a rabbit, but it's egg-shaped, which also reminds you of easter.
Answer: OLDROD
Explanation: The Old Rod will more or less only get you wild level 5 Magikarp in R/B/Y - the Super Rod which you can get on Route 12 (also known as Silence Bridge) is much better for catching Pokémon.
Answer: SHOALSHELL
Explanation: On high tide, you can collect Shoal Shells in Shoal Cave.
Answer: LUREBALL
Explanation: Kurt in G/S/C will make you a Lure Ball if you give him a Blu Apricorn - blue being a color commonly associated with water.
Answer: WATERGUN
Explanation: Water Gun is R/B/Y TM12. It's a weak Water attack which nobody would really want to use seriously in late-game; I don't know why anybody would teach it to their Pokémon.
Answer: MUDDYWATER
Explanation: Muddy Water is basically like Surf (the most commonly used Water attack for competitive purposes - the 'tradition' referred to) except that the attack animation is brown, the accuracy is lower and it may lower the opponent's accuracy. For short, it's a dirtier version of it.
Answer: GOLDEEN
Explanation: Goldeen (derived from 'queen') evolves into Seaking... Blame Nintendo of America.
Answer: CORSOLA
Explanation: Corsola is a coral, and corals can't move, so it is rather puzzling they'd appear by day but somehow disappear at night.
Answer: LOMBRE
Explanation: Lombre have red claws, they dance on Colosseum and XD and their abilities both have to do with Rain Dance.
Answer: LANTURN
Explanation: That was just a reference to paper lanterns. Paper would most likely dissolve fairly quickly in the sea.
Answer: STARMIE
Explanation: Just look at the name... it thinks it's some sort of a superstar. Poor misled thing. =(