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Is there any reference to traditional water Navys in the Imperium or elsewhere in the 40K universe or is it assumed that efficiant Space and Air power have rendered than usless.

If there is any reference do they have a seperate organisation or are they part of other Imperial forces e.g do the Astartes or Imperial Guard have boats that they can use.

They're generally part of PDFs, depending on the nature of the planet.

The book Flesh and Iron has entire regiments of naval infantry, battleships, and aircraft carriers. Also riverboats galore, since it's about Space Vietnam.