The Diatom Filter is designed to operate continuously in salt or fresh water. The main reason we don't recommend it is because most fish will not be able to stand the strain of constantly having to swim against the strong current generated by the Diatom Filter or any other high flow filter for that matter.
Fish need rest and may very well die if they don't get it. Naturally it is up to the individual to determine how much current his fish can tolerate and how much filtration is necessary, depending on the size of the aquarium and fish. I strongly suggest that all power filtration be turned off for a few hours each day unless it is particularly needed at the time. The Diatom Filter will filter out particles and parasitic life forms down to about one micron in size. We are not particularly after the bacteria. We are after the fish killing parasitic protozoan life forms such Ishthyophtririus Multifiliis (Ich), Chilondonella, Myzobulus Sporozoan, Octonitiasis and other Flagellates, Sporozoa, Leaches, Etc.
It is almost impossible to get rid of all the parasites in an aquarium, but with the proper filtration we can keep the population of parasites low enough so they do not harm healthy fish. Medication sometimes helps, but I am a firm believer that more fish are killed by over treatment with medication than any other cause. Proper filtration is the key.
Oxygen molecules are on the order of 4 Angstroms is size and are unfilterable in the general sense of the word. The Diatom will not filter out the oxygen, in fact it actually reduces carbon dioxide levels in the aquarium because of the speed of the impeller (3,000 R.P.M.). Dissolved gases are liberated and allowed to escape at an accelerated rate.
It is quite alright to medicate (if you feel you must) while the filter is running. The Diatom will not filter out the medicine as long as you are not using Super Char in it with the Diatom Powder. When you feel the medication has done its job, simply add Super Char to the filter and the medicine well be absorbed