This probably has to do with the TILE being used by carp and quite possibly, other fishies in the raws. You might want to gve the latter a see-through and make sure that the tile in the raws matches the one that looks like a fish in ironhand.png.
Sorry I'm a noob, I dont quite get what you mean...
Edit: Also, is it possible to make mist/miasma/etc. transparent?
Here's a step-by-step procedure:
1. Go to the data folder thats in your DF installation.
2. Go to the art folder.
3. Double-click on ironhand.png file to open it in an image-viewing progam (usually Windows Picture Viewer).
4. The picture shows the tileset made by Ironhand. Count the number of tiles, starting from the upper-left corner and going right, beggining with the number 0. The last tile on the right should be #15. Look for the tile you would like to use for fish, and then proceed to count towards it using this.
5. When you get to the tile you want, note down the number you counted to in paper, or in notepad.
6. Go to the raw folder in your DF installation.
7. Go to the objects folder.
8. Open the creature_large_riverlake.txt file.
9. Search for the [FISH_CARP]. Once you've found it, look for the tag "[CREATURE_TILE]". This tag should have a number next to it.
10. Erase that number, and write in the number you noted down from counting on the picture file.
11. Save the file and quit.
12. Fire up DF, go to the arena, and spawn a carp in the water.
If you see the carp look like the tile you wanted, congrats! A modder is you!
If it did not work, go through each step again, and check the number that you counted to make sure its the right one.
P.S. For the lazy ones and the TL;DR crowd, the tile number for the fish-looking graphic in ironhand.png is 172.