I've got some old radio gear from the military, and when you're dealing with a 300w uhf transmitter that needs to go into an unpressurized area of an aircraft, you have to go down this same road, because it needs to be AIR-tight (to a large pressure differential), not just WATER-tight.
One unit I have here is a tube type amp. Tubes are NOT efficient. Their solution was to make a hermetically sealed case (complete with pressure gauge and what looks like a bicycle tube valve on the outside. A part of the inside is a heat exchanger, and a fan runs internally to circulate air around in the case. There's a 1x1 hole in the back for intake, and 1x1 hole on the bottom for exhaust. That, along with about 24 1/4" bolts and a large gasket, allows this amp to remain sealed, pressurized, and cooled at 30,000 ft. Note that while there was a fan on the inside exchanger, the unit itself had no external moving parts. The slot you dropped the radio into in the aircraft supplied the moving air into and out of those external holes for the external side of the exchanger.
The old motorola maxtraks were mostly solid-state, but used tubes for their internal PA amp. Instead of a heat exchanger, they used passive radiation for cooling. The power transistors that inverted the AC to run the tubes were bolted onto the sides, were completely covered, but were attached to a large chunk of slightly finned aluminum. It didn't radiate very efficiently, but they didn't generate a LOT of heat, and the plates had a relatively large surface area, so it was enough.
The tubes on the back were a very different story. Normally you cool tubes with air convection, or in much larger applications, with a built-in water jacket. These were placed sideways in the back, and a LARGE hunk of aluminum fitted over them. The inside of the aluminum was curved to wrap around the outer 1/2 of the tube, and be in contact with it. The outside of the aluminum had many large, durable fins. So these tubes were kept cool by passive radiation.
Those maxtraks were made to be tossed (literally) into the back of a squad car and go on high speed joyrides without damage. They were tanks, and used NO air circulation.
I doubt you can use an air exchanger like in my first example, but there it is for reference in case you can use it. You're more likely to go with the second example, and just use a sealed case with a large passive heatsink. You could also just go with the heat pipe and radiator you have for the CPU already, and move that part of it out from the middle a bit, and run the exchanger line(s) out of the main enclosure, exposing the radiator to the outside. That would be fairly easy to waterproof, but most of those exchangers are made of copper and may not fare well when exposed to water. You will also need some sort of a screen / filter to keep the fins clean. The maxtraks didn't care about that, their fins were large plated aluminum, and spaced far apart. Much more durable than a modern heat pump radiator.
You could take inspiration from any modern day solid state amplifier. Even the audio amps would be worth a look, though they don't actually deal with anywhere near as much heat dissipation. (efficiency can get pretty high at audio frequency, and VERY poor at high radio frequency, making good cooling necessary) Many designs use extruded aluminum with fins on the top and two sides. Salvage a chassis off a burned up audio or rf amplifier like this, and go from there. Waterproofing the enclosure will probably be your bigger challenge than cooling.