Located at the mouth of the Weeki Wachee River, Bayport was first settled in the 1850's as a shipping point for cotton and food supplies. The town gained some notoriety during the American Civil War when local blockade runners did very well in getting around the Union fleets that were blockading the larger ports along Florida's coast. That activity spurred the Brooksville Raid in 1864: Union troops marched north from the Anclote River area and faced off against a group of Confederates near Brooksville. The Union troops won the skirmish and then proceeded to burn barns, storage buildings and croplands around Brooksville before proceeding west to Bayport. At Bayport, they sacked and burned the town, sank several boats in the harbor and destroyed the piers and docks.

After the Civil War ended, Bayport was rebuilt and served as the main shipping point for goods from Brooksville until the railroad arrived in 1885. Since then, Bayport has become more of a backwater, retreat-type place serving local fishermen and local families looking for a quiet place near the Gulf. The only business in town seems to be the Bayport Inn, at the junction of Cortez Boulevard and Pine Island Drive.

This being the mouth of the Weeki Wachee River, the estuary and tidal zones are shallow and reasonably treacherous for folks who don't know the area. Hernando County and the Southwest Florida Water Management District dredged the channels and rebuilt the marina and park area at Bayport in 2008. The park area is where the photos on this page are from.

Between 2000 and 2010, the population of Bayport rose almost 20%.