Higher than normal concentrations are called blooms and the toxins in them can kill fish, crabs, and other marine life.
Photos and videos from southwest Florida show hundreds of dead fish in waterways, dolphins washing ashore, and even a beached whale shark in the Sanibel area this July.
Siesta Key is known for its blue water and lively marine life.
This is not the first time red tide has been so intense.
WINK Meteorologist Matt Devitt posted on Facebook about some of the devastation.
Scott directed the Florida Fish and Wildlife Conservation Commission and the Florida Department of Environmental Protection to "mobilize all available resources" to address impacts in Southwest Florida.
"FWC will deploy additional scientists to assist local efforts to save animals affected by the naturally occurring red tide".
"Over the past week, reports were received for multiple locations in Sarasota County, in Charlotte County, in and offshore of Lee County, and in Collier County".
Florida's southwest waterways are now under assault by two different combatants: A red tide bloom from the Gulf of Mexico and a separate toxic algae bloom, which many believe is linked to discharge from Lake Okeechobee.
Members of the U.S. Army Corps of Engineers are working to release some of the toxic water from the lake.
The Miami Herald reported the blue-green algae outbreak had grabbed national attention.
She began treating poisoned birds as early as October.
"With this year's red tide being more substantial than previous years, we must do everything we can to help minimize its harm to our water and wildlife".