Charles Throsby was formally appointed magistrate and commandant of the settlement in August 1805. Except for the occasional soujourn in Sydney he seems to have remained Commandant at Newcastle until September 1808 when Lieut. Villiers was appointed to the position. He still had an interest in the settlement however and returned on at least one occasion.
He resigned his position of colonial surgeon because of ill health in 1809 and became an agent for Sir John Jamison - an early land holder. He took an active part in exploration work leading the party that discovered a land route to Jervis Bay. He is believed to have been the first European to explore the Canberra district.
His valuable exploratory work helped development west of the mountains and he was given large grants of land in reward for his services. 
Charles Throsby has a lasting legacy in Newcastle by the naming of Throsby Creek in his honor.
He died without issue in 1828 -
'The Honorable Charles Throsby
This Gentleman was an old Colonist. In the early stages of the Colony he was on the Civil Establishment as an Assistant Surgeon, and had the honour of being appointed to the Magistracy by His late Excellency Governor King.
Mr. Throsby was a very large grazier, and had amassed no inconsiderable wealth by his extraordinary and patriotic attention to the rearing of stock of a very superior quality. Several years ago he had the misfortune to become a surety to the amount of £5000, more or less, for his friend, the late Garnham Blaxcell Esq., of well known celebrity in these Colonies, but who had to flee the Country, from the effects of mercantile embarrassment, in April 1817.
Proceedings at law were instituted against Mr. Throsby, and only a few months ago the affair was decided to his disadvantage, from which he intended to have appealed to the King in Council. This circumstance is supposed to have operated so powerfully on his mind, as to have occasional mental aberration, in one of which fits, on the morning of Wednesday last, the lamented Gentleman terminated his existence by misuse of a gun, at his country residence.
Advices of the deplorable event reached town on the afternoon of Wednesday and as the people had scarcely recovered from the effects of another catastrophe that had occurred in the morning the melancholy intelligence arrived to produce general petrifaction.
Several Gentlemen have been summoned to effect the last token of respect and friendship by following the remains of the late Mr. Throsby to the silent tomb which ceremony is to take place in the course of this day at Liverpool'.