I am not familiar with such a journey, but I would worry more about the corals than fish because of CITES. The officers you will encounter at the borders likely have never been tasked with a similar situation before. Crossing both into Canada and then back to the US could be problematic. However, how likely is it that you get searched at either crossing? Perhaps show military ID and also wear uniform?
The safest is to check with both US and Canadian customs and get approval or permits for the transport. Make sure to have the ID of the approving officers with you to both borders. I would imagine being in the service you do not want to be caught importing CITES protected animals without permits.
If the livestock is not very rare or expensive it might be easier and less stressful to simply buy new animals at your destination.
Good luck and thank you for your service!