That's what I've been doing, though not 'tried' much as of yet. Discussing with outhers has yielded some interesting results however and at least one other person believes this to be semi-easily do-able with just Prototypes.
From my discussions it seems there's jsut a few things 'needed' to make this work:
---An Ore that can only spawn in-water (I was thinking Undersea Morphite as a possible variant to regular)
---A means to mine said ore (In the case of this, doing much similar to the ore; A miner or set of miners designed solely to be usable in the water, with a land-tile collision preventing them from being placed. If I look into Cargo Ships itself I might find a clue, as the boats are only placeable in-water... so I know that water-only item are able to be made
---Refinement of said ore/ cleaning (For this, I was considering it too be a hook into Angel's Refining, with the Sluicer or Floatation Cell being used to 'wash off' the ores.
---And of course means to collect from the water-miners; In this case, I'd think Bouy models to use as either inserters or conveyor belts, and a tank or some other item to be used as a storage for the item for collection.
The liquid Morphite could also be possible, and Ive seen a mod for underwater pipes.... So perhaps a drill requiring sulfuric acid to 'melt' the 1x1 ore deposit, which produced liquid as an output?