Finding some way to eliminate their Claydol (s) is likely going to be your best bet. Sniping and spreading decks that can do this take away the ability to constantly refill the hand with cards to discard with Dragon Pump, and Kingdra slows down. Power locking from the likes of Gardevoir or Glaceon lv. X would also do the trick, albeit more temporarily, and both of those cards get outsped by Kingdra so they aren't the best bet. If you are able to take out Claydol (s), subsequently Wagering them successfully down to 3 should be especially crippling.
TM-TS 2 is another way to temporarily slow down Kingdra if they rely on quick Rare Candies to get them into play. It can also make it easier to get KOs since you'd only need 50-80 damage on Kingdra as opposed to 130, and the attacker wouldn't even have to have any energy to devolve it.