mechEhere,
I would think any potting compound will work, as long as it is not water soluable, and as long as it is applied properly.
According to my chart here, IP68 must withstand continuous submersion. I do not see a depth specified, but I recall it is something like 2[ ]meters for something like 24[ ]hours. Definitely, you should look it up. Your options are to buy an off-the-shelf IP68 compliant enclosure, or to build a 2m tank to test out your own design.
Find out how much heat you have to dissipate. A ventilation fan will not work, although a circulating fan might. Your electronics designers are going to have to co-operate with you, and at least tell you how much heat you have to dump.
JHG