Riverhead district schools will open Thursday, while schools in the Shoreham-Wading River district will stay closed due to the damage caused by superstorm Sandy.
It was not immediately clear if McGann-Mercy High School would open Thursday, as school officials could not be reached for comment.
All three districts had closed Monday and Tuesday due to power outages and damage caused by Sandy, officials said.
Riverhead schools superintendent Nancy Carney had said two district schools were without power Tuesday, and the Aquebogue Elementary School gym had lost the top coat of its roof.
The Hampton Bays High Shelter is closing down, Southampton town officials said, while the Riverhead High School, Easthampton High School, and Suffolk Community College Shelter Eastern Campus shelters are closed.
The Eastport South Manor High School shelter is still open, officials said.
A state of emergency remains in effect for Southampton Town, including the Flanders, Riverside and Northampton areas.