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If you have high iron content in your water and your sprinklers will be spraying over the sidewalks and onto vinyl siding, you may want to consider running certain zones through the softener. Personally, I already designed my system with 2 manifolds (one on each side of the house) with 2 PVB, and if I wanted to go through the softener with the zones that hit the sidewalk, I would have to add 2 MORE PVB, and decided that I would powerwash if the iron/rust buildup becomes an issue.
My neighbor had a professional installation and he put 3 of the 7 zones through the water softener. The rest of my neigbors completely bypassed the softener. My water pump cycles aprox. every 60 seconds when the sprinklers are on, and I thought that would be rather hard on the softener.
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(1) There are systems (not a standard water softener that uses salt or potassium choloride) that is specific to irrigation systems that remove the rust from the water so your house/sidewalks don't turn red - but they're a couple of bucks. You don't want to SOFTEN the water -- even though it removes a small amount of rust, the PRIMARY purpose of a softener is to remove CALCIUM, not rust.
(2) If your well pump CYCLES constantly during your watering (on/off/on/off/on/off etc.), then your zones were improperly designed (not enough gpm pull on each zone). The ideal situation is for the gpm draw to be such that the pump turns on ONCE when the watering begins and then off when it's done -- a continuous running of your pump. Otherwise, you're going to be replacing that pump much sooner than you probably would like.