Water  and underwater resources

Water

As you should  already have discovered you need water to grop crops. You can collect buckets of it and  throw the water onto soil plots to water them. Throw the water on the line dividing twoplots and you might be able to water two plots at the same time. Throw the water on the junction of four plots and you might be able to water four plots at once.

Watering large numbers of plots becomes tedious but it is possible to automate the process. That's described in crops2.html and crops3.html

Refining metal requires you to have water containers available. You can create these using a craftbot from buckets of water but it's much easier to use a vehicle fitted with a vacuum pump and chest to collect the water you need. Bluebird, an amphibious vehicle I describe in items.html, is an example of this. You can use the same technique to collect oil and chemicals from pools of these substances.

Glue Clams

Early in the game you'll want to expand your storage by creating chests. At that point you'll discover you need to get glue as an ingredient. To make this you must go swimming with your hammer and use it to break giant clams to get the glue ingredient. You'll find you get 1 - 4 glue clams from each clam. 

Oil

There are oil leaks underwater which can be harvested and processed in crafting machines to make fuel. They are quicker to harvest than clams since you can swim over the leak while holding down the right mouse button.

Slugs and Snails

(but no 'puppy dog tails')

 

Glowslugs

If you pick up a glowslug while underwater and take it back to your base you can feed it cardboard - made from scrap wood. It will then produce glowslug poop which you can use to make glowsticks and batteries.

Snails

If you pick up a snail while underwater and take it back to your base you can feed it eggplants. It will then reward you with random goodies. Stop feeding it and it will escape.

On Water

This is Bluebird. It's named after the boat piloted by Donald Cambell. The man who once held both land and water speed records. Bluebird is fast, both on land and water, but like Cambell's bluebird, it's a little unstable at speed and liable to take off and crash upside down if you give it too much power.

 

Bluebird is great at transporting caged farmers from the haybot campsite and works well at collecting water, oil and chemicals.
Construction details at items.html#bluebird

Under water

The machine you use to quarry rock can be used underwater too. There's lots of the rock outcrops underwater. The problem is you have to breath. The Fant mod allows you to create an air generator (which looks suspiciously like an air conditioner). Place it under your seat with the right settings and you won't have to keep surfacing for air.
Construction details at miner.html with the necessary modification at miner.html#underwater.