I honestly don't have any experience with anything that would or wouldn't be environmentally safe for something that's actually in the water. But did have a couple thoughts that may help a little.

The first one is to cut the infected leaves off and either burn them or put them into your garbage can. Definitely don't compost them if you're a composter. After the cannas have flowered you can cut the stalks down and get rid of them.

In the meantime, once you've cut the 'bad' leaves off, mix a little dish detergent in water and spray the rest of the plant. Since rust spores are soil based, and spread by winds/breezes, this may help to keep it in check temporarily so that you can enjoy the blooms.

Being in Florida, I would imagine that they will put out new growth and that you'll get flowers again if you're going to just cut them completely back.

Jenna

Someone on GW once recommended cinnamon for a fungicide. I tried it and it worked. It is also said to repel ants but I haven't tried it for that. I don't think it would hurt to 'experiement' on one plant to see if it works on rust as well.

I'd go to home depot and buy a spray bottle of air duct cleaner. It's a solution of chlorine dioxide that is meant to be sprayed into your HVAC air ducts to kill mold / spores / bacteria and what not. Cl. dioxide solutions are also used as a commercial food prep / produce disenfectant and I recall reading somewhere that some grape grower was trying it on there grapes. It should probably be safe for the plant (it is NOT like a bleach solution) - but I'd try just one leaf to make sure first though...

(it's also used as a water purification agent so it will not be toxic to the lake)

From the net:

"Vegetables washing

Chlorine dioxide is an excellent product for washing vegetables. The ability to kill spores, viruses and fungi at low concentrations is essential.

ClO2 is a proven product that can be used to solve several food-related problems. It does not affect taste, odour or appearance. It is safe to use and complies with food regulations. Below are some examples where chlorine dioxide has been applied.

Apples: control of E.Coli and listeria bacteria's
Potatoes: protection against "late blight" and "silver scurf"
Lettuce, celeries and onions: compared to hypochlorite the vitamin-c content resulted higher and the potassium content lower
Citrus fruits: protection against "green mould" and "sour rot" proved to be successful at several pH values, low concentrations and limited contact time. "

Just make sure it doesn't take out the leaf as well!

I let mine go, at the end of the season they do look awful but I have tons of butterflies and they come back fine next year. Some years the rust seems to be more of a problem then others, like when we have a tropical storm or hurricane. Good luck! Tally HO!

Thanks to all of you for your helpful answers. As they've bloomed themselves out now, I'm going to wade into the water and cut down the worst stalks and burn them. Some new shoots are coming up and are about knee high now. Next year, I'll probably try the cinnamon suggestion before moving on to anything stronger. Thanks again.