Add a bit of bleach to the fresh water tank
and run the water through all the fresh water lines. The main problem is you get critters living and multiplying in the lines, not just the water tank. Essentially you need to shock treat the water lines and drain the tank completely. Also, if you have strainers or any charcoal or other kinds of filters between the tank and your faucets and fresh water fittings, remove prior to flushing
the lines. Once the lines are thoroughly flushed, replace the old filters or elements with new ones and put back in any faucet strainers you may have removed.
As Deepfrz recommended, check out Peg's latest post as well if using raw water
not fresh water for flushing the head