The Department of Education ended Jose Maldonado-Rivera's tenure status after the drowning, but allowed him to continue to lead the school on a probationary basis.
On Tuesday, the DOE ousted Maldonado for allegedly putting his nanny on the payroll and giving her a free place to stay.
Following the drowning incident, education department officials began looking at prior allegations made against Maldonado by parents and teachers.
In this particular instance, the principal allegedly hired his nanny, with whom they say he was having an affair, to work as parent coordinator in 2008.
"Looking at the full history of Dr Maldonado's conduct, we have determined that his repeated failures in judgment make it inappropriate for him to continue as Principal of Columbia Secondary," Natalie Ravitz, communications director of the DOE, said.
Dr. Gary Biester will begin as Interim Acting Principal at the school on Wednesday. He is the current Assistant Principal at the High school for Math and Science and Engineering at City College. He has a PhD from Columbia University.