A water molecule is made up of one oxygen atom and two hydrogen atoms why is it considered a pure substance

A pure substance is any substance on its own. For example, sand is impure for containing lots of different substances. However, diamonds are mostly pure for only containing one type of substance.

Whether a substance is pure or not doesn't relate to a substance's molecular structure, but different molecules in a substance. Water by itself is only H2O, therefore it still pure.

Water is not an element but a compound for containing different elements, however it still pure.