I once was working at a salmon/trout farm and during my time there we were unlucky enough to be notified by the government that one of our tested specimens (allways before putting them out in waters) was tested positive for an Epizoo classed virus. That means virus with mortal possibilies that can transfer between animals and also to humans. In other words very nasty stuff to release that can affect humans and lots of wild animals.
That meant we had to totally put out all of our stock with electricity or large doses of tranq and then desinfect all of our gear, tanks and dry out and do the same to the ponds and even electrocute and do the same to the surrounding areas streams etc.
Not very pleasant. However for desinfecting the gear we used Virkon. A substitute for killing basicly any virus, bug or bacteria and it comes in various forms.
http://en.wikipedia.org/wiki/Virkon
The dams and the surrounding area we "killed" with this:
http://en.wikipedia.org/wiki/Calcium_hydroxide