Does anyone know how to make a container/boat waterproof? When I place it in water, the water simply goes through the closed object.

you can't,   you'd need the water to have collision properties which it doesn't. 
you would have to achieve this by green screening.

so for example,  let's say you had a guy floating in the box on the ocean,  you'd want half the box to be covered with water,  -  so you film the whole box submerged,   then do a second film of the same box, without the water green screened with your character in it.   You import that green screen into your video editor,  overlay the image onto the flooded box,  then mask half of the green screened box,  so half that box looks submerged,  but the half with the character in it is dry.

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Ok thank you! I guess the simpler solution is to compose the scene so that such angles are not visible in the final render.

Animate the boat with the water hidden.
Render
Make the water visible, then place a green screen tile in the areas where the water shows in the boat without masking the water outside the boat.
Render
In a video editor, layer both renders with the water clip on top and use the green screen effect to reveal the dry boat.
Done.