We get build-up of iron rich bacteria in our well. Eventually, this leads to an unpleasant odor in our water (especially when the water has not been run for a while) as well as slime in the toilet tank, etc. The odor is much more noticeable in the hot water. I'm not sure if that's because the bacteria like the hot water better or because the warmer water releases the odors better. Anyway, I try and shock the well about once or twice a year to stay on top of this problem.
My question is what to do about the water heater. Since the problem is more noticeable in the hot water, I want to make sure that the hot water pipes and water tank get addressed as well (the water heater tank is 80 gallons), but I also know that a high concentration of chlorine can corrode rubber seals, etc. In the past I only flushed the system through the cold water pipes but then Idrained the hot water tank to get rid of any bacteria in that water. However, I felt that the smell returned pretty fast because I wasn't killing the bacteria sitting in the hot water pipes or the walls of the tank. Also draining and refilling our hot water tank is a pain because our well has a low refill rate and if I let it fill our 80 gal tank as fast as it can, I will run the well dry and kick up a lot of sediment - not to mention being bad for the pump. Of course, I can't see exactly how fast it is filling inside the tank, so I would end up filling it extremely slowly.
A few years back we had an outdoor hot water spigot installed for an outdoor shower. So these days, I flush the system through the hot water tank then run all faucets (hot and cold) until I smell the chlorine. Now I've got chlorine water in all the pipes. After letting it sit for a day, I flush through the hot water tank again until it's chlorine free again. This can take a long time, since I don't want to exceed 1.75 GPM and the 80 gallon tank will only slowly return to a no (low) chlorine state since there will be mixing in the tank.
So, I feel like either way is a poor choice. If I don't run through the hot water system, I feel I'm not addressing half of the problem, if I do run through the hot water system, I feel the chlorine may be doing damage somewhere in the system. So what's the best way to address the whole system, without causing unnecessary damage? Is what I'm doing OK, or should I be doing something else? I think when this water heater goes, we'll probably go to a tankless water heater, but until then...