You can find "waterproof crimp connectors" easily enough. (Google for some examples.) For this low voltage, low current application, crimp connectors sold for telephone wiring will be just fine.
I've made waterproof splice connections by soldering the wires, slipping a piece of heat-shrink tubing over the splice, and filling the tube with silicone caulk. After the caulk had set, I applied heat to shrink the tube, compressing the caulk against the splice. Very waterproof, but overkill for my needs.
Commercial connectors would have been a lot less hassle.
I'd solder the connections and use shrink tubing, because I have that stuff and it works (good for decades).
There's not really a problem with 12 getting wet,anyway, unless you have it underwater in a metal tank and cause electrolytically driven corrosion.
If you are bringing the wire through a wall, make a loop so the drips run off the bottom rather than run into the wall fitting.
Make the splice or connection and use shrink tubing to insulate it from the elements. If done properly, it will do the job for you.
Simplest, for a 12V. low load motor, just use crimp connectors
or wire-nuts and just 'pot' the splices in 'Plumbers Goop.'
( NOT suitable for higher voltage or load.)
you could try spray-on bedliner from an auto parts store, or you could coat it with rubber paint (like for pliers' handles)
I want to connect this small water pump
http://www.ebay.com/itm/261149897470
to a 12 volt battery. The battery will be indoors and the pump will be outside. I want to make the wire connection to the extension wires to be water proof. How do I do that? What will I need to use?