On a larger scale, think of a river or stream polluted with trash and debris. If you want to filter out the trash you can take a net and place it across a point in the river. The trash will be too big to pass through the holes in the net but the water can still pass through. What happens is the trash collects at the point where the net is and the trashless water passes through.
This is basically what a water filter does but on a smaller scale. You essentially have a barrier that allows water molecules to pass through but is too small to allow microorganisms, dirt, debris, and other harmful or undesirable particles to pass through.
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