The Tocobaga people first lived in present-day Clearwater. Around 1835, the United States Army established Fort Harrison in honor of William Henry Harrison on this site during its campaign against the Seminole. The fort was situated on a bluff overlooking Clearwater Harbor, which became part of an early 20th-century neighborhood named Harbor Oaks. University of South Florida archaeologists excavated the site in 1962 after having found a underground ammunition bunker by Mark Wyllie while planting a tree in his yard. 

The area’s population increased after Congress enacted the Act of Armed Occupation of 1842, which offered 160 acres (0.65 km2) to anyone who would have weapons and cultivate the land. Early settlers included Thomas Stevens, James Stevenson, John Sever, and Bertram McMullen, who exploited the area’s plentiful resources. In the nineteenth century, the region was known as Clear Water Harbor. The region’s name is thought to have come from a natural clear water stream nearby. Numerous additional freshwater streams dotted the bluff and flowed into the bay and harbor.

Originally Clearwater was part of Hillsborough County. The first road was built connecting the cities of Clearwater and Tampa in 1849, which dramatically lessened the previous day-long commute between the cities.

During the American Civil War, Union gunboats raided the community’s resources because most able-bodied men were off fighting for the Confederate Army. The town was developed in the late 19th century, triggered by the completion of the first railroad line into the city in 1888 by Peter Demens. Clearwater, FL, was incorporated in 1891, with James E. Crane becoming the first mayor. The tourist destination’s popularity as a location grew after railroad magnate Henry B. Plant constructed a sprawling grand Victorian hotel named Belleview Biltmore just south of Clearwater in 1897.

By the early 1900s, Clearwater’s population had grown to around 400 and nearly 1,000 in the winter. Clearwater’s oldest existing newspaper, the Clearwater Sun, began printing on March 14, 1914. Clearwater was reincorporated, this time as a community, in May 1915. Clearwater was designated the seat of Pinellas County, which then separated from Hillsborough County in 1912. In 1915, a causeway was constructed across the mouth of Clearwater Harbor, connecting it to the city and Clearwater Beach to the west. Clearwater Beach, although located on the separate barrier island of Clearwater, is part of the city of Clearwater and fronts the Gulf of Mexico. A new, much higher than before bridge now arcs over the bay, replacing the former drawbridge; the connecting road is part of State Road 60 and is called Clearwater Memorial Causeway.

Clearwater, Florida, accommodated members of the military who were going to Europe or into the Pacific for the better part of World War II. Every hotel in this vicinity, including the Belleview Biltmore and the Fort Harrison Hotel, was converted into a barracks for new recruits. Vehicle traffic was regularly interrupted by troops marching through city centers, and nighttime blackouts were methodically used to confuse potential threats of enemy bombers. The remote and isolated Dan’s Island, now known as the highrise-dominated Sand Key, was an Air Corps fighter-bomber target.