The fire broke out at about 3 p.m. in Island Recreational, a pool supply store at a strip mall on Hicksville Road in Seaford.
A total of five stores were burned by the fire and three buildings were evacuated.
By late Monday afternoon, firefighters had declared the blaze under control.
"Everybody is using their self-contained breathing apparatus. There was an unknown type of chemicals in the building. We keep taking air quality samples, and so far everything has been negative," said Robert Schmidgall of the North Massapequa Fire Department.
The tests showed there are no dangerous levels of chemical contamination in the air.
There were major delays on the Northern State Parkway as a result of the fire investigation.
One firefighter suffered a minor injury.