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Normally there are lots of gaps and spaces between soil particles, and in this space is oxygen which diffuses into the roots of a plant. When the soil surrounding a plant becomes over-saturated with water, all the air spaces fill up, which essentially suffocates your plant. Without oxygen supply the plant's roots will die back.
Root rot can also be caused by a fungus or bacteria which eat away at the roots, like when you get gangrene, causing the roots to die.