I sterilize my boots, waders, and equipment with a 10% solution of color-fast chlorine and filtered water. Leave it on for 30 seconds, then rinse thoroughly. I do this to my gear as well.

I didn't realize this was a problem. Most biotics cannot survive long out of the water, and are sensitive to sudden temperature changes. The exceptions would be viruses, which can survive just about anything.

I guess the major concern right now is the spread of Whirling Disease, which affects trout and salmon. (Brown trout can carry it, but are immune to the disease itself). It is a parasite that was introduced to the US from Europe in the 1950s. It breeds in tubiflex worms, and spreads by spores in the water, and by direct contact with other infected fish. It is mainly transmitted by direct fish-to-fish contact, but is is possible that the spores could be transferred by equipment, however slight. The chlorine treatment I described above will eliminate the threat. Quaternary ammonium compounds such as 'Bright Water', 'Roccal-D', and 'Parvosol' are also effective treatments for your gear. They are available at most Veternarian supply stores, and some Feed Stores.

This will kill Mud Snaills, Didymo, hydrilla, milfoil, ich, finrot spores, Whirling Disease spores, most parasites, amoebas, euglenas, paramecia, quagga, and most bacteriums, and make life hard on some viruses. You can follow up with a phenol spray and rinse to kill remaining viral agents.

As long as you rinse your gear after treatment, there is little danger of putting chemicals into a new stream.