Was this site known before the Mosul dam was built? It's only been about 40 years.

It seems they knew there were hundreds of sites to be inundated and there was an effort to investigate as many as they could before the damn was built https://www.jstor.org/stable/25182504

It's very common that both historical artifacts and natural wonders have been consumed by reservoirs, I suspect it would be almost impossible to avoid this.