What types go well together in a Pokémon deck?
Check out the World Champion Decks to see which type synergies the top-ranked players are using

World Champion Decks have been released since 2004 and contain non-tournament-legal cards matching the decks of several high-ranking players in the Pokémon World Championships. 

Regarding Water types specifically, the only Water decks released between 2004 and 2017 were: 


Pure-Water decks (x7)
Water/Electric decks (x4) 


Therefore, I think it's fair to say that Water and Electric go well together, possibly better than others.

Check out which type synergies are used in Theme Decks

You might also check out other Theme Decks that have been released to see other combinations that might go together. There isn't any guarantee that they'll be good, but presumably the deck synergies that are released will be functional, and types that work well together will probably get multiple releases.

For instance, there have been more Water/Electric and Water/Psychic decks released that Water/Fighting decks, and no Water/Darkness or Water/Fairy decks. Therefore, I'd infer that the former are probably more likely to go well together than the latter, since the Pokémon Company keeps producing decks with those synergies.