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I am not on well water, I am on city water. It's a pretty clear cause and effect, I can have the system on (main irrigation valve open and the valves before and after the PVBA open) with clean water in the house. But if I am running a zone then very clearly brown water comes out of any of the faucets.By any chance are you on well water?
I see, you are suggesting that maybe there is sediment in the main water system and only the sprinkler system is active enough to aggitate the existing sediment?You might leave the sprinkler system out of it, but duplicate its flow by opening all the faucets on sinks and bathtubs, and if you aren't seeing brown water by then, open some outdoor hose bibs.
Talk to the water department, and see if they have a schedule of flushing the mains, which gets rid of sediment in the system.
By any chance are you on well water?
Some wells seem to end up having some buildup on the steel casing. A newly installed sprinkler system can cause the water level in the well to drop considerably, and in doing so, exposing this buildup to air for the first time in many years. The buildup falls off the casing and into the water, and the pump forces it into the plumbing. I can't imagine it would go on for very long, or we'd be hearing more about this phenomenon. The best solution might be to try and remove the discoloration with a cartridge filter in the house plumbing.