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I thought they tend to pipe far out and discharge as far below the surface as possible, since there is a lot of surface life and it is less damaging this way.

Ships (with long submerged pipes) would be prone to weather events and generally less reliable than an installed pipe. Perforation would be prone to clogging from build up so a nonstarter I would expect. Adding flex tubing and a relocation robot would be a maintenance headache as well. Not sure there is an easy optimization.

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Ships wouldn't need a long submerged pipe. It'd just need a small hole like a bilge drain or maybe a live well on a fishing boat. Just let the boat cruise around slowly draining back into the ocean.

As for surface life, I'm no oceanographer, but is that really the most vulnerable place? The surface is where fresh water rain meets the ocean, so that would dilute the salinity during storms. However, there's nothing to say that another pump couldn't be pulling from the ocean and mixing the brine into that so it's diluted before and not just pouring brine straight into the ocean

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I think your sense of scale is off. 90% of sea life is on the surface. 0.029% of ocean water is replenished from rainfall annually. Desalination concentrates are absolutely toxic to life. The current daily volume of brine discharge would require more than half the tankers in the world to be filled and discharged every single day. They would of course not last long with such a routine.
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Is that a total for all of the oceans? I understand that as a whole, rainfall is literally but a drop in the ocean. However, confined just to the local area where the rain is falling, the area’s salinity has to change. Just like adding the the desalinated brine is a minuscule amount compared to the whole ocean, it has large effect locally.

Regardless, it is totally possible to reintroduce the brine back to the ocean in a way to not be a shock to the local area. We have just chosen to make it harder on ourselves for some illogical reason.

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In my opinion you are hand-waving away a difficult engineering problem and proposing a naive solution as if it would solve a problem that has already been partially solved, by rejecting all the work that has already been done on it. Don't dump on the surface, don't burn millions of tons of fuel a year to do it, study what has been done and improve on it instead.
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If you want to be really clever about it, maybe the ship is powered by the brine.

https://en.wikipedia.org/wiki/Osmotic_power

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I like this! Though I’m not sure the math works. That page says ideal efficiency for that system would be something like 0.75 kWh/m^3. Compared to 4000 to 5000 kWh/m^3 of diesel. Now we don’t need to be efficient since the point is to use up our “fuel” and we don’t need to cary cargo for this to make sense but with numbers like that, I don’t think our boat will be able to make enough power to move at all.
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