The water typically goes much deeper than the bottom of the lake. So the rock and sediment at the bottom is just sitting on top of a mix of rock, sediment, and water. So the water is pushing on all sides of the material – not just on top – so the top layer is just suspended in the water, so it is easy for a fish or something to kick up sand or mud at the bottom of a lake.
Now, that material still has greater density than the water, which is why it sinks to the bottom. And as more layers build up on top of it, then those layers of other material start to pack it down. Eventually, those layers can end up deep underground (like 2,000 feet), and over a few million years the pressure of the ground above turns it into stone.
Lakes themselves are generally some of the briefest living geographical features. They may appear and disappear over 100,000 years, while it takes tens of millions of years to wear down a mountain.
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