Police cordoned off convenience stores with yellow crime scene tape including the Wanna Save and Hillcrest Store in the city's East Gateway neighborhood as they searched for the illegal substance.
Super Sonic, 724 Missouri Ave., and Danny's Tobacco Shop, 1621 Gulf to Bay Blvd., also were part of the sweep.
Investigators filled 49 black trash bags with brightly colored packages of the incense some with names like "Mr. Nice Guy" and "Scooby Snax" from the Hillcrest Store. The value of the 18,000 seized packages is estimated at $300,000. Illegal weapons were also found during the search.
Officers also seized $15,000 cash during the raids.
The raids were the culmination of an investigation kicked off months ago when undercover police purchased illegal drugs at some of the stores, said Rob Shaw, Clearwater Police spokesman.
"The goal is to get some of these things off the streets," Shaw said. "We've been doing this about a year now. Originally we served all of these stores notices that it was no longer going to be legal to sell these kind of stuff on the streets and in the stores."
Synthetic marijuana is illegal in Florida after state leaders banned the substance a year ago.
The fake drug is also partly to blame for the death of at least one person in Clearwater.
Logan Kushner, 19, drowned in a creek near Kapok Park in January 2012 after smoking "Jazz."Officers also arrested four suspects during the sweep:
Remon Aziz Farg, 33, from Wanna Save, was arrested and charged with sale of synthetic cannabis.
Christopher T. Dolu, 30, from Wanna Save, was arrested and charged with possession of synthetic cannabis, distribution of synthetic cannabis and sale of synthetic cannabis.
Tarek Gwazwan Allababidi, 19, from Super Sonic, was arrested and charged with two counts of sale or delivery of a controlled substance and two counts of possession of controlled substance.
Jean Hanna Bitar, 57, from Danny's Smoke Shop, was arrested and charged with two counts of sale/delivery of controlled substance and two counts of possession of a controlled substance.