Oxygen is also a big factor.
Roots need oxygen to survive, they can’t get it from the plant’s vascular system.
In hydroponics, water is constantly circulated and enriched with oxygen. Even without active circulation, oxygen can diffuse from the surface. Enough for fish, enough for plants.
In waterlogged soil, not only is the plant’s foundations weakened, but there isn’t any air circulation or even diffusion because of soil covering the top layers.
Plus, waterlogged soil promotes growth of fungi and bacteria, since there’s both moisture and organic matter to munch on. In pure water, there is very little for anything to colonize.
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