Mostly it’s specific to the species of plant and what environment it needs to thrive. Generally, over watering cause roots to soak in unmoving stagnant water which facilitates rot compared to a living viable water system; there’s more rot in a bog or swamp than in body of running water like a pond, lake or river.
So not all plants can grow in with their roots submerged in water. Many will just die.
That being said, for those plants that CAN grow in water or soil, care needs to be taken. Although roots look the same to our eyes, roots that are grown in water and grown in soil are different, and if you take a plant that was grown in water and put it into soil it very well can kill the plant. You need to transition the plant properly from one to the other.
Second, you might think that something like hydroponics just means growing food in water, but it is actually a little more complicated than that. Typically hydroponic and aquaponic systems have water levels that cycle up and down. So a plants roots will be submerged for awhile, then the water will drain and the roots will be in air (or the media), and then they will get submerged again.
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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