Bonita Springs is located at 26°20′59″N 81°47′27″W / 26.34972°N 81.79083°W / 26.34972; -81.79083 (26.349654, -81.790937).

According to the United States Census Bureau, the city has a total area of 106.2 km² (41.0 mi²). 91.4 km² (35.3 mi²) of it is land and 14.8 km² (5.7 mi²) of it (13.95%) is water.

The city is located on both Estero Bay and the Gulf of Mexico. The area referred to as Bonita Beach is located on a road-accessible barrier island (Little Hickory Island) that lies between the Gulf of Mexico and Estero Bay. The Imperial River flows through the downtown district of the city and empties into Estero Bay.

The city is the northernmost city on the west coast of Florida that has a tropical climate, having a mean January temperature of 65 °F (18 °C). (Fort Myers Beach directly to the north has a January mean of 64 °F (18 °C) which gives it a subtropical climate.

 Points of interest

• Art League of Bonita Springs - an arts organization that hosts both local and traveling art exhibitions, arts classes and other community events. 

• Bonita Beach Park - a 2.5-acre (10,000 m²) beachfront park that features a boardwalk and swimming area. Sand dunes and coastal vegetation surround a gazebo and 8 picnic shelters. 

• Barefoot Beach Preserve Park - is 342 acres (1.38 km²) of natural land and one of the last undeveloped barrier islands on Florida's southwest coast. It is located on the border of Collier and Lee Counties and accessible by Bonita Beach Road.

• Little Hickory Island Beach Park

• There are also 10 beach accesses with public parking located up and down Bonita Beach.

• Bonita Springs is located west of Corkscrew Swamp Sanctuary, a significant Bald Cypress reserve under management of the National Audubon Society.

• The northern border of Bonita Springs is shared with Lover's Key State Park, a 1,616-acre (6.54 km²) park made up of four barrier islands. The park features nature trails for hiking and bicycling, a canoe launch, kayak and canoe rentals, acres of unspoiled mangroves and miles of pristine beaches. A haven for wildlife, the islands and their waters are home to West Indian Manatees, bottlenose dolphins, roseate spoonbills, marsh rabbits and bald eagles.

• The Everglades Wonder Gardens features a large collection of Florida wildlife including exotic birds, panthers, alligators, flamingos and bears. The facility, originally opened in 1936 as both a wildlife exhibition and a refuge for injured animals, also boasts a botanical garden and a natural history museum.

• The Naples-Fort Myers Greyhound Track is located in Bonita Springs.

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