In 1792, Shortland came back to Australia with Hunter. Hunter had been made Governor of New South Wales and Shortland was First Lieutenant on the "Reliance". Other officers on the ship were Matthew Flinders and George Bass. In 1797 Shortland found and named the Hunter River while searching for escaped convicts. He explored the area which is now the city of Newcastle. He made the first charts of the harbour. Shortland was given grants of land at Liberty Plains and Bankstown. He also served as a member of the Criminal Court in Sydney. He missed the excitement of navy life and in 1800 he returned to England on the "Reliance".