How do we know the natural abundance of isotopes on Earth?
Because we can sample the environment with great precision
You seem to assume that we can't know the exact makeup of a sample unless we already know the components. This is wrong. Mass spectroscopy can reliably measure the exact mass of every isotope in a sample and the relative abundance of each. If, for example, a sample of sea-water is measured, we can reliably tell the exact proportion of all the hydrogen isotopes and all the oxygen isotopes in it.
Given that his is possible, estimating the true natural abundance is a matter of statistical sampling. Ocean and river water is fairly well mixed so this is easier than it sounds (at least when there are no processes that radically alter the isotopic composition). So we have a lot of samples, for example, from different oceans and different locations in those oceans. Given that, we can be fairly confident that the isotopic composition doesn't vary a lot and, therefore, we can get a good estimate of the &quot;natural&quot; abundance of each isotope.
But the techniques we use are precise enough to notice that there are some (small) variations in that composition. Some processes do (very slightly) alter the isotopic ratios. Evaporation tends to happen slightly faster for lighter isotopes, for example, as do some biological processes. Some of those processes are temperature dependent leading to the ability to identify the ambient temperature preset when some fossils were alive by measuring the ratio of oxygen isotopes in them.
The key point is that we do have tools that can measure isotope ratios very precisely. So we know the ratios in any sample very precisely. With a very large number of samples, we can generate a reliable picture of the typical abundance of each isotope which is what we refer to as the natural abundance.