You can pound pile into shallow water with a fraction of the impact of that in deep water. You can also de-water the area around the pile in shallow water. They could also be vibing in the steel pile instead of pounding it. Vibing reduces the overall sound pressure peak. Data is fairly scarce on sound traveling through earth into water, so as of now, NOAA and USFWS are not asking for mitigation on this kind of pile driving. For the most up to date info on pile driving, look at the Washington State Department of Transportation web site.
http://www.wsdot.wa.gov We have a ton of data on pile driving because of our ferry operations. Working in Eastern Washington, I am not the expert on this, but do know enough to get myself into trouble. I would consider the biologists in our Ferry Department the premier experts on this subject. So if any of you have questions about it, please feel free to contact them.