A stream picks up a lot of pollutants and such, but unless it's the slowest moving stream in the driest season, the water volume spreads problems so thinly that it barely matters. I recall a still, greenish pond a couple of days before the rains started in Gabon. We fished it anyway and caught Epiplatys singa, a nice surface killie. They were wearing woolen coats of fungus/bacteria, and it had eaten their tails off. But fish caught nearby in the streams that were still moving were clean and healthy.
Even puddles - we caught a breeding group of a killie in a 2 foot long, 10 inch deep roadside pothole. But overflow from a nearby waterfall probably changed the water in that "tank" every ten minutes. Nature likes its water changes.
We're dealing with something of enormous complexity. The life in the tanks I have must be amazing, but I can only see a tiny percentage of it. I remember as a kid using my sister's Christmas gift toy microscope on tank water, and the show was fascinating. 
And we take out a test kit, measure the nitrogen cycle and think we know about the water. We think that tells us when the water needs to be changed. It's like tasting a dry spice to know if the meal's cooked.
The solution to this incredible complexity is delightfully simple. Change water on a regular schedule.
Our lives aren't simple, and life gets in the way of our plans. A few years ago, my fishroom was running like a dream. I had a great balance of feeding, growth, plants, water changes (weekly), light stocking and fish choices, and the room was happening. A family member was diagnosed with cancer, I became her caregiver, water changing dropped to once every 3 weeks and within a couple of months, I lost almost half the species I'd kept for years. We fall ill, family members fall ill, we get stuck with tons of overtime, special projects start - if we neglect our tanks, they die. If I seem hardline about needing to change water, it comes from hard experience. 
What do we do? What we can. I'm not quite as young as I used to be, and there's always a sword dangling over our heads as we age. You and I, 
@Magnum Man , have discussed stocking before. You like to fill those tanks with fish. I find doing that very tempting, but we both really LIKE our fish. If life gets really busy, we have to figure out workarounds. Mine is more tanks lightly stocked - most of the time at around 1/3 of what you like. 
You like weird fish, and are great at trying to keep new things. That has its risk, as those fish are often not well known in the hobby because they are delicate. Those beautiful African tetras you love? They were decimated here during the Nurse Gary period. Shoals became individuals who lived a long time, to show me what could have been, I guess.
Sometimes life makes us drop back into survival modes, and our fish have to hang on til the rainy season arrives for them. But it has to come, as soon as it can.