Organic Matter in Well Water

Noticed some organic matter in our well water so began to clean the system. At which time I also noticed a failed check valve near the water tank. It was removed and replaced. Also at this time I decided to check the water coming directly from the well.
When the pump first starts the water has a lot of organic matter. After running for a few seconds it starts to become cleaner and by 1-2 minutes is very clean. If I turn the pump off for ~ 24 hours and then start get the same results.
Since the well is ~ 230 ft deep am guessing that the organic matter is due to a leak around the well cap. Should add that the well cap is below the ground. Did a search but only found one posting. I only recently discovered this problem so do not know if it only occurs during or shortly after a rain.
Appreciate any comments, suggestions or tips on "state of the art" techniques for sealing below ground well caps.
Gene OHara
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