Once you have the tank and lines and faucets cleaned don't admit any contaminated water back into the system.
Just because you don't drink it bad water can drastically affect your health.
Staph and a lot of other nasties can infect cuts and ears and even uninjured skin.
Put a good whole house filter on the incoming line.
Use fresh water chlorine like sold at CW and Wal Mart, that won't taste like laundry bleach, in the tank.
Change the water, if not used every so often.
City water is not clean in most cases. It is filtered etc and filled with a whole lot,of chlorine, to hopefully kill the nasties. It is tested to keep it at accepted levels, or so we hear but some city water, taste like.... and even discolored and they add floride and such too it.
Filter it and put back drinking water chlorine.