Water-types are my 2nd favorite, right below Dragon.
In fact, I typically use a mixed Dragon/Water Team when I'm not using Legendaries, as it helps deal with Ice-types (although Freeze-Dry can be a bit of a problem, nowadays).

Like Dragons, Water-types both have few weaknesses, and work well against most opponents (even Steel-types).
Unlike Dragons, there are a TON of Water-types, so 2 different all Water Teams can be very different from one another.

1. "Make it Rain!"

The core of any good Water-type strategy is using Rainy Weather. If using Legendaries, your best bet is using Kyogre, but for non-Legendary Teams, this can be more difficult.

You'll want to use a Damp Rock, but the main problem is if you're opponent keeps using Sandstorm, or worse: Sunny Day.
In Sunny Weather, a Water-type Team can lose to a Fire-type Team, so you MUST be persistent, and not allow yourself to be stuck in Sunny Weather.

One technique is to make sure you have ways of taking advantage of other Weather Conditions, like teaching Blizzard to some of your Pokémon, or using Water/Rock-Types.

And of course, in Rain, you can take advantage of many powerful Abilities, such as Swift Swim, or the Hydration+Rest combo.

2. Freeze-Dry

Believe it or not, I'd say the biggest threat to Water-types (in Gen 6 and beyond) is a single, Ice-type move: Freeze-Dry.

This is not only because it does 4× damage to many of the strongest Water-types (Gyarados, Kingdra, Swampert, and Ludicolo, just to name a few), but also because there are few secondary Types that can help protect against it (only Ice, Steel, and Fire).
My advice is to use a Yache Berry on 1 of your more vulnerable Pokémon (like Kingdra and the others), and to bring at least a couple of Water/Ice-types, preferably that have Thick Fat (although Thick Fat certainly isn't necessary).
If you like (and have) Empoleon, or Volcanion, they can help with this, as well.

3. Water and Ice

Aside from Freeze-Dry, and the Weather, you basically only have to worry about Grass, Electric, and Dragon Pokémon.
Ice-type moves are learnable by almost all Water-types, and help deal with 2 of those.

Usually, Ice Beam is your best choice, but I personally prefer Blizzard.
Not only because it can hit multiple opponents, but also because of how it can't miss in Hail.

There are other great choices as well, including Icy Wind (great if your Pokémon aren't super fast), Ice Fang/Ice Punch (for more Physical Water-types), and Avalanche (an awesome Physical option, although it's hard to get Water-types with this if you don't have HG/SS).

4. Mix it up

Water-type Pokémon can have VERY different weaknesses, depending upon their secondary type.

Because of this, you'll definitely want a Team with many different secondary types, such as Water/Dragon (these were originally only weak against Dragon, although they are now weak against both Freeze-Dry and Fairy-types as well), Water/Ground (only weak against Grass and Freeze-Dry, and immune to Electric), Water/Grass (weak against Flying, Poison, Bug, and Freeze-Dry), and Water/Steel (weak against Electric, Fighting, and Ground).

Also, this allows you to take full advantage of many other types of moves (besides Water and Ice), giving you much more variety on the offensive side of things as well.

5. Water-type moves

In general, I'd go with Scald, rather than Surf, unless you're doing a Double/Triple Battle combo, like Surf+Storm Drain.

For Starters, you'll definitely want Hydro Cannon, and (for those that can learn it) Muddy Water is a great alternative to Surf (since it can't hit your Teammates).

Also, Aqua Jet is a nice move, and it's interesting to combine it with Storm Drain, as well.
Brine+Super Fang is another nice combo, although it's not perfect.
(If your opponent has an odd number of HP, it doesn't work right, although it's not usually a big deal, IMO.)

And (if it's an option) Dive is a great, often overlooked move, and IMHO, even better than Waterfall (although Waterfall definitely has it's advantages) and Aqua Tail (the only reason to use Aqua Tail is if you can't use Waterfall for some reason, IMO).

And Razor Shell, Liquidation, and Crabhammer are all AWESOME Physical moves, although not available to many Pokémon.

6. Abilities and Held Items

I doubt I could cover everything in this blog (I won't even try to cover Stats/Natures in it), but in general, Abilities that take advantage of Rain, such as Swift Swim, Hydration, and Rain Dish are good, as well as ones that work in combos, like Storm Drain, and Water Absorb.

As for held items, damage reducing Berries are always good, as are the many Water move enhancing items.

Even though I mentioned it elsewhere, I'll mention my Mega Sharpedo trick:
Have a Sharpedo with Speed Boost use Protect on the first turn, WITHOUT Mega Evolving.
Then, next turn, Mega Evolve it.
The result is a Mega Sharpedo that is 1.5× faster than normal, the equivalent of it holding a Choice Scarf.