It’s usually not the water that’s the problem, it’s the mold and bacteria that grows when the soil is damp for long periods of time.
Mold and bacteria need water, oxygen, nutrients, and surface area to grow.
In soil, there’s nutrients and oxygen readily available and a lot of surface area to promote growth. Damp soil provides the water.
Letting the soil dry out between waterings dries the mold/bacteria out, killing off most of it and keeping bacteria growth under control.
In a glass of water, there’s not much nutrients and oxygen, and also importantly very little surface area. Only the surface of the plant roots are available for bacteria growth. A full-water environment doesn’t make for ideal bacteria growth conditions.
Changing the water once a week or two can keep algae growth down, and that’s easy enough.
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