One part of it comes from recent fossils. Some older species are actually present in the fossil record, and in sufficient numbers that we can compare size distribution. We have Nile croc fossils from >5 million years ago (exact same species), and more recent fossils of other taxa, and all seem to be around the same size.

Another is from complete fossils, like those magnificent Archaeopteryx fossils. If they shrunk after burial, either the bones would separate from each other as each bone shrank, or some unknown force would have to pull them all together as they shrank in a strikingly uniform way, despite the tremendous pressure from the surrounding dirt/rock holding them in place.