I believe this thread needs a little more information. You said you have a submersible filter. This leads me to believe that the entire thing is under water? If that is the case, there beneficial bacteria that convert ammonia and nitrite into less toxic nitrate are only functioning as a small fraction of their maximum potential because they need to be in an oxygen rich environment to thrive. Since your bacteria are woking at a minimum capacity I would use the pond water because you want to keep as many of them as you can. If the filter media is getting so dirty that you need to use a jet to clean it, i might suggest that you need to clean the filters more often, or, increase the size of your filter. Also, you asked what to do if your tap water is high in nitrite. Well, if that is the case, you dont have much choice but to continue to use it. And if that is the case, you NEED as much of the bacteria as you can get to help proccess the toxic nitrite. I would not be willing to kill them off each time i rinsed the filter. I am interested to know if you test your water, and if so, do you use test drops or test strips? And what are your levels of ammonia, nitrite, and nitrate? If the first two are always zero and nitrate is under 40 you really dont have anything to worry about but if your pond is registering ammonia and nitrite or you have high levels of nitrate, i would highly suggest getting a bigger filter, feeding the fish less, removing some of the fish, etc.