Physical Characteristics. Putnam County is east of Gainesville and north of Ocala, and is bordered by Flagler, Volusia, Marion, Alachua, Bradford, Clay, and St. Johns counties. The county has 732.88 square miles of land and 94.40 square miles of water for a total of 827.28 square miles. The average January temperature is 58.6 degrees fahrenheit, and the average August temperature is 81.7 degrees fahrenheit. The average annual rainfall is 50.74 inches. History. Putnam County was established from St. Johns and Alachua counties in 1849 and named for Benjamin Alexander Putnam (1801-69), lawyer, soldier, judge, member of the state legislature, and first president of the Florida Historical Society.