In the 18th century the watershed for the Hillsborough River was covered in old growth forest of bald cypress, longleaf pine, and sand live oak.
After the construction of Fort Brooke at the mouth of the Hillsborough River settlers began moving into what would be the Tampa area .
This allowed the shipyard to be surrounded by good quality shipbuilding material, as well as protect it from storms and weather.
During the American Civil War in 1863, Union forces attacked and burned two ships: the steamship "Scottish Chief" and the sloop "Kate Dale" that were moored at the shipyard for maintenance work and to load cargo for their roles as blockade runners, both ships owned by James McKay.
In 1909, the Federal government funded the dredging of the Hillsborough River to twelve feet from the mouth to Jean Street Shipyard (then known as the Tampa Steam Ways Co.).