In 1861 he was appointed Surveyor-General. His early years in the role were very difficult, especially his efforts to help establish settlement in the Northern Territory by supervising the establishment of the pastoral leaseholds that continue to the present day. Pastoralists were hit by a major drought in the middle of the decade and complained severely, with many forced to move even relatives away from their cattle stations by the end of 1865. Goyder was also faced with the despair of his wife, Frances Mary Smith, who suffered the loss of twins at birth during George's long travels in the outback.