Bonnie's impact was minimal. Throughout the Caribbean Sea, the storm mainly caused light rainfall; and in Florida, rainfall caused flooding and minor damage. The tropical storm caused a tornado outbreak across the Southeastern United States, killing three and causing over $1 million (2004 USD) in damage. Bonnie is most notable for making landfall on Florida the day before Hurricane Charley struck.
The tropical wave continued to move rapidly to the west-northwest, until it reached the western Caribbean Sea. While south of Cuba, the system slowed down to regenerate convection, and it re-developed into a tropical depression on August 8. Operationally, the system was classified a tropical wave until a day later. The depression moved through the Yucatán Channel, and intensified into Tropical Storm Bonnie on August 9 while 70 miles (115 km) north of the Yucatán Peninsula.
Bonnie continued to the west-northwest; late on August 9, the storm presented a 9-mile (15-km) wide eyewall, a very unusual occurrence in a small and weak tropical storm. Bonnie quickly strengthened while turning to the north, a directional shift caused by a break in the mid-level ridge. The storm briefly weakened late on August 10; it re-strengthened again the following day to attain a peak intensity of 65 mph (105 km/h). Soon after, strong southwesterly wind shear disrupted the storm, causing Bonnie to weaken again. On August 12, Bonnie made landfall just south of Apalachicola as a 45 mph (70 km/h) tropical storm. It quickly weakened to a tropical depression, and accelerated northeastward through the southeastern United States. After paralleling the Georgia, South Carolina, and North Carolina coastlines, Bonnie lost its tropical characteristics on August 14 to the east of New Jersey. Its remnant low continued northeastward, making landfall in Massachusetts and Maine and continuing into Atlantic Canada.
In combination with the threat of Hurricane Charley, Bonnie forced the evacuation of 154 oil platforms and 32 oil rigs. The stoppage of production was equivalent to over 1.2 million barrels of crude oil, or 0.2% of the annual oil production in the Gulf of Mexico. Natural gas reserves were also limited. The lack of gas production due to the storms was equivalent to 7.4% of the total daily production in the Gulf of Mexico.
Early forecasts for Bonnie indicated that the storm might make landfall as an 80 mph (130 km/h) Category 1 hurricane. In response to the threat, fifteen shelters in seven northwestern Florida counties were put on standby. In the hours before landfall, two shelters were opened, four were put on standby, and health and cleanup teams were deployed to the area. Parts of Gadsden, Wakulla, and Levy Counties issued voluntary evacuations, and numerous schools were closed. In anticipation of the threat, Florida Governor Jeb Bush issued a state of emergency.
In Florida, Bonnie produced up to 4.1 inches (104 mm) of rainfall in Pace, with peak wind gusts of 42 mph (68 km/h). Bonnie was accompanied by a four-foot storm surge; moderate wave action caused slight beach erosion. Rainfall and storm surge flooded roads, forcing the evacuation of 2,000 residents in Taylor County. The winds downed trees and caused scattered power outages. A tornado in Jacksonville damaged several businesses and houses.
Bonnie spawned a tornado outbreak across the Mid-Atlantic. One such tornado in Pender County, North Carolina destroyed 17 homes and damaged 59 houses, causing three deaths and $1.27 million in damage (2004 USD). In Stella, Bonnie generated a waterspout that struck a campground, damaged nine trailers, and wrecked small boats. A tornado in Richlands damaged several houses as well. In South Carolina, tornadoes across the state damaged nine homes. A suspected tornado in Danville, Virginia destroyed the roofs of several businesses. In South Carolina, rainfall peaking at 6.07 inches (154 mm) in Loris caused flooding across the state. The flooding, including a one foot depth along U.S. Route 501, washed away a road and a bridge in Greenville County. In addition, 600 people across the state were left without electricity.
In Pennsylvania, the remnants of the storm dropped up to 8 inches (200 mm) of rain in Tannersville. The rainfall caused the Schuylkill River to reach a crest peak of 12.89 ft (4 m) at Berne. The flooding blocked several roads across eastern Pennsylvania. In addition, Bonnie produced gusty winds, leaving thousands without power from downed power lines. In Delaware, the storm dropped up to 4 inches (100 mm) of rain, forcing 100 to evacuate from the floodwaters. The flooding closed part of U.S. Route 13, and an overflown creek in New Castle County caused moderate flooding damage to stores. In Maine, moisture from the remnants of Bonnie produced heavy rainfall, with localized totals of up to 10 inches (250 mm). The rainfall flooded or washed out roads across the eastern portion of the state. In Aroostook County, near the town of St. Francis, the rainfall caused a mudslide, narrowing a county road to one lane.
Bonnie, as an extratropical low combined with a frontal system, continued to produce moderate rainfall in Canada, peaking at 3.5 inches (90 mm) in Edmundston, New Brunswick. The rainfall caused basement flooding and road washouts; slick roads caused a traffic fatality in Edmundston.
Because Bonnie hit Florida immediately before Charley, damage between the two storms was often difficult to differentiate. President George W. Bush responded to the storm by declaring much of Florida a Federal Disaster Area on August 13, 2004. Because the damage was minimal, the name Bonnie was not retired; it is on the list to be reused in the 2010 Atlantic hurricane season.