Several ways, but it all comes down to keeping track of your ins and outs. We know what each molecule weighs, and we know what each atom weighs. Since you can’t have fractions of an atom (we’re not doing nuclear here), there’s only certain combinations that can give you the right molecular weight.
For something like water you can combine known quantities of hydrogen and oxygen into water (by burning them) and measuring how much oxygen or hydrogen is left. Whatever got used must be in the water.
More complex molecules take more work to create but if you just keep track of what you started with and what you have now you can track where all the atoms must be.
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