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I had the same situation on my first roof.  we took the fish out of the pond and covered the area several feet past the edge of the pond.  the home owner trated the water with a chlorine neutralizer which they use when they add tap water to it.  I would guess every one with a fish pond would have that on hand.  Anyway the fish are still living and the homeowner was satisfied with the job.

Kevin dont forget to add your signature buddie. We just like to know who everyone is. I havent had this predicament before so from experience I cant help you. What I have heard is the tarping of the pond, like said already. I remember reading that one time the tarping didnt work. If just washing a roof dont be so crazy with the spray. Use common sense. Take your time on that side of the house. Bag the downspout, though I never have once yet. You should be ok? (I'm using a 2gpm delavan). Just use common sense with your wash. Always think about what is going where.

Maybe also add a pole for the middle of the pond and then tarp it, kinda making a tent. It should help from pooling of the SH and any chance of the SH leaking thru.