Bigger the body of water is, more likely it is to have drainage from the surroundings which bring sediment and nutrients. Along with currents caused by moving water or by wind to mix it all.
Also the kind of ground matters a lot. Nice sand and gravel ground doesn’t have much stuff to start mixing in to the water. While clay and dirt dominated landscapes do.
But if you look at why two bodies of water, which could be equally clear and clean looking, they might be so for totally different reasons.
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