In 1873, the St. Croix Railway Improvement Company combined the three settlements into South Stillwater, which was incorporated as a village in 1881.

[7] Like its northern neighbor Stillwater, the early economy of Bayport centered around the lumber industry.

The Andersen Corporation prospered in Bayport, becoming the largest window and patio door manufacturer in the world.

Experts at the time considered the prison to be one of the most modern penal institutions in the world.

As of 2010, the prison housed about 1600 inmates, who are counted as Bayport residents for census purposes.

The maximum security Minnesota Correctional Facility - Oak Park Heights opened just beyond Bayport's western boundary in 1982.

[9] Due to its location on the St. Croix River, Bayport has long been associated with boating.

The Bayport Boat Yard, located just south of the Andersen Corporation, built several well-known steamboats.

According to the United States Census Bureau, the city has a total area of 1.75 square miles (4.53 km2), all land.

[1] Bayport is located in the Stillwater Area School District (ISD 834).