Try to rebuild well pump

This AM I noticed dirty water in the house plumming. We have a deep well (>200 feet). When I went into the basement to check on things, I could hear the chlorine pump (which runs when ever the well pump is on) running and it was hot. I also noticed that the chlorine tank had gone down quite a bit (it was just the other day). Based on this I am pretty sure something was running all night. It could have been a toilet or possibly the backwash on the water softener or greensand filter. So based on this I am sure the pump was running for a long time, and since the chlorine tank had gone down I think water was flowing. I have in the past had a the condition were the water level in the well has dropped to a point were the pump could not trigger the pressure switch and the pump would continue to run, which is also the case now, but have not see the water be "dirty". I have turned the pump off and will give it a day to recover, but I am wondering if this is something new since I have not see the water become dirty in the past. It is possible that the pump was running quite a bit longer than it had in the past. Any thoughts on this? As I said I have had cases in the past when the water level dropped to a point were the well would not shut off, but have not see the "dirty" water. BTW: With the pump off the pressure in the tank is holding.

We live in Mexico. This is the first house we have lived in with a septic system. I don't know much about our system nor how septic system work in general. We are in this house almost 3 years. Every year when we enter rainy season (now) funky odors come from the floor vents in the master bath. In the farthest corner of our lot, along a retaining wall is a 3" PVC tube which I believe is the vent for the septic system. It is just normal PVC with no cap. When it rains here - almost every night - it can rain 2-3". I'm wondering if the PVC tube - which raises perhaps 15 feet or so from the ground - has gotten filled with water and therefore there is no venting (except into the house). Does that make sense ? I was thinking of drilling a small hole in the pipe to see if water leaked out to confirm my theory. Then if I'm correct I was thinking of adding some sort of cap to the PVC pipe. Any thoughts appreciated. Edit : btw - I have never done _anything_ in terms of septic maintenance. Never added chemicals etc. When we bought the house the previous owners gave us some architectural docs for the house - including the septic system (which I think was called a septic 'farm'). I believe (from memory) there is no metal or plastic 'tank'. There is a bunch of underground rocks - with no way to access anything without starting to dig.