John Goodwin was District Surgeon for Invermein in 1839, however was to resign from this position at the end of September 1840

Later in the 1840's John Goodwin became enveloped in controversy and disgrace. An altercation with Reverend John Morse over land that had been granted for the erection of a church was the beginning of lengthy legal proceedings. The Church land had been taken for a burial ground by Reverend Morse who then exacted a fee of £2 for internment and an additional 10/6- for fencing. When John Goodwin refused to pay 10/6-  (presumably for a fence around the grave of his child) he was sued for it, the decision going against him.

In September 1844, amid the usual pomp and ceremony afforded to visiting  justices,  Justice A'Beckett arrived in Maitland in readiness for the Quarter Sessions. Among the cases to be heard - assault, horse stealing and forgery was the trial of surgeon John Goodwin. After a lengthy trial, the jury found Dr. Goodwin guilty of libel after a letter written by Goodwin was read in evidence. It had been written to the Bench of Magistrates at Scone accusing Reverend John Morse of the theft of a writing desk and denouncing Magistrate Joseph Docker in a bitter invective. Justice A'Beckett stated that Goodwin had 'bestowed upon Reverend Morse the grossest epithets of abuse, ridicule and a strain of sarcasm of which the humour was completely overpowered by the scurrility.'

Petitions were made on behalf of Goodwin - one by Reverend Morse  - in which Goodwin was spoken of as a member useful to society by his talents, the friend of the poor and the teacher of their children and the father of a large family in no thriving circumstances. Although Justice A'Beckett felt every desire to mitigate the sentence (perhaps due to Goodwin's 'fancied wrong in connection with his lost child'),  the judge felt unable to yield to the benevolent wishes of the petitioners or his own feelings as' it would be an injustice to the public and to the miserable wretches who had received sentence at the bar.'

This was not the last of the matter for John Goodwin. He complained very much of his incarceration and petitioned the Lord Bishop of Australia to no avail. Finally he appealed to the Legislative Council where his petition for redress was read. The Colonial Secretary however opposed its reception, thereby concluding the case.

Dr. Goodwin was involved in another Court case in 1847 when a patient of his, Norah Hatherall of St. Aubin's died during her confinement. He was indicted for having feloniously injured her to such an extent as to cause her instant death and by attempting to deliver her while he was intoxicated. Although other witnesses testified to him being intoxicated at the time and Dr. Fowler that a dose of morphine had been excessive, both Dr. Liddell and Dr. Sloan gave their opinion that Norah Hatherall's death was caused by exhaustion from a long and difficult delivery. It was stated by the attorney for the defence that a man placed as Dr. Goodwin was, a medical man living in a district so scattered that possibilities for consulting seldom arose, must not have his actions or his practice scrutinized so severely as men living in large towns having ample time and opportunity for caution and advice before proceeding to act in difficult case, but must be protected.

After retiring for a few minutes, the jury returned a verdict of not guilty and Goodwin was discharged.

In 1849 John Goodwin was undergoing insolvency proceedings. He appealed in the Supreme court against a refusal of his application for a Certificate and the following the following information was provided: