Hi, welcome to TFP! Well water frequently has iron in it, which will turn the water brown as it oxidizes. If you are able to have iron free water from another source you could drain and refill the pool, but as you top off the pool with well water the problem will return. You will need to use a sequestrant to keep the iron in suspension so it does not oxidize and turn the water brown.
Keeping the water properly chlorinated will eliminate the bug problems, and it will kill algae so your water does not turn green.
In order to keep the water balanced you will need a high quality test kit, such as a Taylor K2006 or a
TF 100 . A good test kit is an investment in your pool, and is just as important as your pump and filter for keeping the water clear.
Is your pool an intex style pool without a skimmer? Does it have a sand filter or a cartridge filter? If you do not have a skimmer, then the easiest way to clear the water will be to drain and refill the pool. The brown will filter out eventually, but you would need to keep the filter running 24/7 and frequently rinse the cartridges or backwash the sand. If you do have a skimmer you can put some fiberfill pillow stuffing in it to help catch the oxidation. When the fiberfill turns completely brown rinse it out and reuse, or rotate with fresh fiberfill. Do not pack the skimmer tight with fiberfill. It needs to be loose to maintain water flow to the pump. Filtering out the oxidation will take time, possibly a week or more.
When the water is clear, either by filtering out the oxidation or refilling the pool, use sequestrant to prevent the iron from oxidizing again. Test your water and use
http://www.troublefreepool.com/calc.html to calculate how much chlorine and other chemicals you may need to add to balance the water chemistry.
Read this link for more information on water chemistry.
ABCs of pool water chemistry