The canal was completed in 1968 and the dredged material was used for a levee 10 to 20 feet high on the southern side. The levee was broken into 50 spoil mounds restricting water flow to the southern marsh. Prior to construction or the canal the Panhandle served as a source of freshwater for Florida Bay. Impounding the system altered its natural hydrology and subsequently may have affected water quality throughout the marsh and northeast Florida Bay.

Restoration of the Panhandle began in 1995 to mimic historic water flow patterns through the southern marsh. Spoil mound removal was completed in November 1997.In order to understand how the restoration will impact the system, a joint study between Florida International University and the South Florida Water Management District began in May 1998 and will continue for 3 years.
From September 1997 through April 1998, a pilot study was performed to gain baseline data from before levee removal and immediately after removal.