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Can you put plants that grow under water into the system to oxygenate water as well as give smaller fish such as mosquito fish an area to live and hatch?

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I personally haven't done it, but I don't see any reason why you couldn't.  Depending on the type of fish you have, as they get larger they may begin eating the plant.  Also, you would want to be sure that pieces of the plant don't clog up your plumbing.

For cover for mosquito fish they do very well with Hornwort. Also Duckweed.  What kind of plants pretty much is ruled by your fish species. Are Mosquito Fish(Gambusia) your primary fish or are they to feed your others?  If they are for food fish then some cover is advisable, and Hornwort is almost essential.  

My primary fish will be channel catfish, But where I live there are a million mosquitos and I've read a post from someone else that their aquaponics system eradicated the mosquitos around their farm. I don't think catfish would eat the mosquito larva so I'm thinking of setting up a tank for mosquito fish but they need plant cover. So I thought if there were good oxygenating plants it could help the system as a whole.

Lots of places for Gambusia with hornwort and duckweed. You could put this in with your catfish too if you have surplus.

Actually Gambusia by themselves are fry safe but duck weed and hornwort will help you to have more, catfish will pick off the Gambusia so they need replacing,  many will survive. 

Good luck,

Jake

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