I cannot speak for the water quality where you’re camped. And evidenced by a recent thread, some folks are far more finicky than others when it comes to drinking water.
But reasonably you should have no issues (gastrointestinaly) using the fresh water supply filtered or unfiltered.
With your black tank flusher. Try this occasionally. Do what ya did but also run it a while with the valve closed so a greater volume of water flushes out faster. You’re likely to see it remove more “matter” than just leaving it open while flushing. (Which is generally fine as well. Imo)