So I'd like to suggest something that may or may not work. Make your aquarium. Make two channels connected to it - one so that water from the ocean comes in, another under a grate (which is itself under a hatch) that takes the water back out. The way out, if you're not using a hatch, will be floodgated, as will the way in. Again, hatches are ideal here as they close faster.
Water comes in from the ocean, and brings fish with it. Water flows right out again, but the grate leaves fish inside. As they get water pouring through the whole time, the fish shouldn't airdrown - not that it's an issue if you use undead fish. Once you've reached the requisite amount of fish, close the hatch over the grate, and, once the aquarium fills up, close the hatch letting the water in.
The hatch over the grate, by the way, is so that you can stop water from leaving, but whatever you do, fish stay in. Also, this, if it works (feel free to shoot down and flame me as you see fit if it doesn't), should apply to rivers and brooks as well. If you have one of these as well as an ocean, than good. More variety in fish.
Why yes, I
am way too lazy to do this myself. Anyways, good luck to all involved, feel free to try this, and, ofcourse, rage away as you like if it turns out that I've failed completely
Oh, and I think that's the biggest post I've made on this forum. Glee.