If you can its best to declorinate the water first befor it goes to the tank, but if you add your declorinator to the tank and then add water right into it thats ok too. jsut make sure the tempature is close on, and that the pH change isnt going ot be drastic either. I wouldnt worry about thr bacteria because your only changing a small percentage of the water, and from what iv herd its pretty resiliant, aslong as its not a huge change in chemestry or tempature. if you want to be extra safe jsut tunr ur filter off wile you add the new water. declorninater works basicly instently anyway.