If that aluminium heat spreader will not come off then I would have a go at lapping it flat to remove the raised decorative embossed bits and leave a flat surface for your cooler to interface with. You would then also be able to use a proper thermal compound like MX5, rather than thermal pads. This will significantly improve performance.
Given you obviously do not want any particles of aluminium to find their way on the pcb or under the spreader while you are lapping, you'll want to go to town wrapping the exposed pcb with electrical tape on all sides, including sliding some as far as it will go under each side of the spreader. This will still leave a gap around the spreader though where particles could still get through to the components under the spreader, so to finish off the insulation I would run a small bead of silicone sealant around all sides of the spreader to basically fill that gap. So you should end up with the exposed top of the spreader for lapping, with everything else sealed so no particles can get anywhere they shouldn't.
Once this is flat you could even then consider if you could get away with attaching another heatsink to this with thermally conductive adhesive, or more clamping, and then runs fans on it, rather than attempting to water cool. This is if the heat spreader cannot be removed, because if it can I would be looking to do that first and see if a bigger heatsink can be fitted directly, which obviously deals with the complexities of getting filtered water in to this, which I see as the main issue with the set up.
However, if that water cooling plate is just a bare channel inside, i.e. it doesn't have any tiny fins, or convoluted paths like a PC water cooling block would have, then than reduces the risk of running it with filtered pond water I would imagine. I would however design the mounting system as something you can disassemble easily so you can strip the cooler down to clean the insides after each trip. I think I would also include a flow meter in there somewhere with a light to indicate if the flow has reduced or stopped, so you know its time to bring it ashore. On a PC forum everyone here is going to be paranoid about the merest particle of algae or water scale in a water block, but that is because it is built once and left for months. As long as you can strip down to clean you only have to worry about it blocking within the scope of a single outing, as long as you can take it apart to clean.
As regards fitting the cooler I would go with the mini mg-clamp method with some padding on the underside.
edit: The more I look at that cooler in your first pic the more it looks like it will be a single block of aluminium with two straight holes drilled in line with the two ports, going some distance down the block, then probably a single hole drilled at 90° to this on the side we can't see which is then either plugged or welded. This gives a very simple single U shaped channel inside the block. It also means you won't be able to take it apart to thoroughly clean as there is nothing to come apart, so you maintenance of it will probably just be to run high pressure mains water through it, backwards and forwards. At least you won't need to take it off the pcb to do this.
Given you obviously do not want any particles of aluminium to find their way on the pcb or under the spreader while you are lapping, you'll want to go to town wrapping the exposed pcb with electrical tape on all sides, including sliding some as far as it will go under each side of the spreader. This will still leave a gap around the spreader though where particles could still get through to the components under the spreader, so to finish off the insulation I would run a small bead of silicone sealant around all sides of the spreader to basically fill that gap. So you should end up with the exposed top of the spreader for lapping, with everything else sealed so no particles can get anywhere they shouldn't.
Once this is flat you could even then consider if you could get away with attaching another heatsink to this with thermally conductive adhesive, or more clamping, and then runs fans on it, rather than attempting to water cool. This is if the heat spreader cannot be removed, because if it can I would be looking to do that first and see if a bigger heatsink can be fitted directly, which obviously deals with the complexities of getting filtered water in to this, which I see as the main issue with the set up.
However, if that water cooling plate is just a bare channel inside, i.e. it doesn't have any tiny fins, or convoluted paths like a PC water cooling block would have, then than reduces the risk of running it with filtered pond water I would imagine. I would however design the mounting system as something you can disassemble easily so you can strip the cooler down to clean the insides after each trip. I think I would also include a flow meter in there somewhere with a light to indicate if the flow has reduced or stopped, so you know its time to bring it ashore. On a PC forum everyone here is going to be paranoid about the merest particle of algae or water scale in a water block, but that is because it is built once and left for months. As long as you can strip down to clean you only have to worry about it blocking within the scope of a single outing, as long as you can take it apart to clean.
As regards fitting the cooler I would go with the mini mg-clamp method with some padding on the underside.
edit: The more I look at that cooler in your first pic the more it looks like it will be a single block of aluminium with two straight holes drilled in line with the two ports, going some distance down the block, then probably a single hole drilled at 90° to this on the side we can't see which is then either plugged or welded. This gives a very simple single U shaped channel inside the block. It also means you won't be able to take it apart to thoroughly clean as there is nothing to come apart, so you maintenance of it will probably just be to run high pressure mains water through it, backwards and forwards. At least you won't need to take it off the pcb to do this.
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