Initial rust when pump turns on

I have a deep-well pump with a large whole-house filter and a water softener. I've noticed that when I replace the filter, the water is initially nice and clear. However at some point (I believe when the pump turns on, or maybe when the bladder is inflated?) a few gallons of very rusty water come out. This rust is trapped by the filter, but this is causing me to have to replace the filter every month or so.

Is there some setting or other method where I can have the well discharge the first few gallons outside of the plumbing system, or is there something that needs to be cleaned of rust in the well pump?

Thanks in advance.

Maybe rusty pipes?

It sounds as if the main supply pipe from the pump to your tank/filter/softener may be rusty inside. The effect you describe is essentially what happened to the old galvanized iron pipes in my house, even on a city water supply. If the water doesn't run for a few hours, or days, rust forms inside the pipes and one must flush a few gallons to purge the rust particles before the water runs clear. If that's the case in your system, consider replacing the pipe with new galvanized iron pipes, or better yet, copper or heavy duty PVC plastic. The water in my bathrooms used to run rust red when I first turned on the faucets, but having replaced them with a mix of copper and plastic pipes, it now runs clear right from the start.

I've heard from folks in my area that some years ago a load of bad galvanized iron pipe was imported into the U.S. from Korea. It was poorly galvanized and was missing copper in the alloy. Pipes that should have lasted 30+ years were rusting out and leaking in less than 15 years in many tract houses in the San Jose, California area, and elsewhere. Perhaps you have some of that kind of material in your system.