Marion County is generally composed of rolling hills, some high and some low. The majority of its trees consist of live oaks, pine, and palm trees. Marion County is considered the southernmost county in North Central Florida, and the northernmost county in Central Florida.

It is about a two hour drive from many of Florida's major cities; Orlando is 75 minutes to the southeast while Daytona Beach is about 90 minutes to the east. Tampa is about 75 minutes to the southwest. Jacksonville is roughly a two hour drive northeast. Miami is about five hours to the southeast. Fort Lauderdale is about a four-hour drive from Marion County.

Marion County also has three large lakes at its opposite borders. Orange Lake is in the far northern part of Marion County, near the border with Alachua County. Lake Kerr is in the northeastern part of the county, near the town of Salt Springs, which is near the border with Putnam County. Lake Weir, the largest of the three, is in the far southern region near the border with Lake County. Part of Lake George is in Marion County also.

Marion County is inland, centered between the Atlantic Ocean to the east and the Gulf of Mexico to the west. Because of this, Marion County is not affected as much by hurricanes as the more coastal counties to its east and west are. However, tornadoes are a major threat to this region of the state. Although Marion County is not near either of Florida's coasts, it is situated slightly to the west. Therefore, it takes a little less than an hour to get to the Gulf of Mexico while it takes about half an hour longer to get to the Atlantic Ocean.