The ink in the markers is often made from several colorful chemicals that we excrete again. When the water draws into the coffee filter paper by capillary action, it dissolves and carries some of the ink molecules with it. The larger, heavier molecules in the ink move more slowly than the smaller, lighter ones, so they move with the water at different speeds and settle in different places as the water moves upward.

You will probably find that the darker inks such as black, dark blue and brown work best because they tend to be made from many more colors.

This is the basis of paper chromatography, which is one of the most useful techniques chemists have for separating chemicals from a mixture!