What prompted the work was the fact people found sea shells and fossil shark teeth on mountains and in mines and embedded in rock everywhere.
The theory at the time was that the shells just grew in the rock, basically 'magically'.
Steno's theory that the shells were deposited in sedimentary layers in water that later turned to rock and were uplifted took about 120 years to be accepted.
Science has proven slow to accept what in retrospect appears completely obvious. 120 years to decide shells embedded in rock identical to living shells didn't just 'grow' there.
Fossil evidence for the aquatic ape theory, if it exists at all, would be found about 300 feet below sea level (the sea is higher now).
The ability of humans to dive deeply in the ocean and swim so well suggests it was important for survival at some point in the past. And it doesn't seem unreasonable that early humans lived along the coasts and ate fish and other sea life.
I'm not sure why this idea is so controversial, really.