"Chlorine doesn't kill as much as you think. Those of use in the Metro Milwaukee area experienced that a few years back with the Crypto outbreak. It ended up killing my dog actually (older dog that had kidney failure due to the crypto...)"
One way to take care of crypto is with a filter. It is about a 3 micron organism (the cryptosporidium oocyst).
The Milwaukee outbreak occurred because of failure of the chemical pretreatment system necessary for effective filtration with a sand filter.
The Harmsco 1 micron absolute filter has been approved for removing at least 99% of the crypto oocysts. It actually removes more than 99.9%.
http://www.harmsco.com/uploads/pdf/harmsco_polypleat_catalog.pdf
In addition to the Milwaukee outbreak, there was a serious crypto outbreak at Seneca Lake State Park in New York in 2005. There were more than 2000 cases before they were done. It was in a recreational water application; not drinking water.
Crypto is usually not fatal for healty people but it is deadly for those with compromised immune systems.
Legionella is another organism that is resistant to chlorine, because it is often protected by a biofilm.
The protection provided to organisms by biofilm and dirt is why filtration is considered an essential part of the process of treating surface water. Lakes, ponds, rivers, and shallow wells and springs are considered surface waters.
If you are using surface water for showers or any potable use, you should filter and chlorinate it.