I have no evidence that there was an aquarium aboard the Ark, but there was likely some sort of tanks that were used to separate fresh water and salt water aquatic life and in one of those was likely the two Trilobites as the remainder were lost in the catastrophic burial as documented in this article.
Must have been really big tanks to put in all the sharks and whales and such. Plus having to go catch all of them and bring them back to the ark.