Brown well water

I woke up Saturday morning to find out my toilet was running all night and I was out of water. The water came back pretty quickly but was now brown. It is now Monday evening and the water is still brown It seems as if the Coldwater is clearing up but the warm water is still brown. My well guy said yesterday to let it rest. How long do I let it rest or do I run it to see if it clears out? The pressure is good but the water is still brown so I'm wondering when I start to panic and ask him to come over or if I should give it another day or if I should just run it