Given the fact that flounders are bottom feeders, we can speculate that they would not be adapted to live in headwaters. Generally, headwaters are often small and cold streams which flow rapidly over hard ground. Given that generalization, such conditions will not favor flounders, which feed on small creatures they catch by ambush. Flounders are able to change their skin color to match the sea bottom. There are no known flounders which live farther inland than estuaries, a fact which supports the idea that headwaters are not suitable for flounders.
In truth, it is difficult to define "headwaters", although the general description given above holds in most cases. The term is used figuratively when a lake or swamp is the source of a river.