In an ecosystem there are fish which eat, and then this food is decomposed. The decomposed food is turned to ammonia. In the presence of oxygen, nitrosomonas bacteria turns the ammonia to nitrite. Then, the nitrite is oxidized by nitrobacter bacteria to turn into nitrate. Plants then take in this nitrate to remove from the water. If anything, removing the plants should be ok since contact with the atmosphere helps clear the nitrate as well.