Gardner's first charge was St Andrew's Presbyterian Church,[2] which opened in Conway Street, Birkenhead, Cheshire in 1840.

[5] The position was offered to Gardner, who accepted, and with his wife, three children and a servant sailed to Adelaide aboard the Condor, arriving in March 1850.

[6] He took advantage of the ship's stopover at Port Melbourne to preach in the John Knox Church, Swanston Street.

Shortly after his arrival, Gardner initiated the purchase from (later Sir) John Morphett of the prominent site on the corner of North Terrace and Pulteney Street, appointed English & Brown[8] as architects and builders, laid the foundation stone for what was to become Chalmers' Church on 3 September 1850[9] and held the first service there on 6 July 1851.

[4] He was one of the signatories to the deed which signified the union of the three branches of the Presbyterian Churches in Adelaide on 10 May 1865: John Gardner (Chalmers Church), Robert Haining (St. Andrew's, Wakefield Street), John Anderson (Strathalbyn), James Gordon (Gawler), James Lyall (Flinders Street), W. Davidson (Clare), Alexander Law (Mount Barker), and James Moddich (Mount Pleasant)[12] After 18 years' service to the Adelaide congregation, Gardner accepted a call to St. Andrew's Church, Launceston, Tasmania, which at the time had a very strong and wealthy congregation.

[2] South Australia was at the time experiencing a financial recession, and the Adelaide church was unable to compete even remotely with the very generous £600 (perhaps $100,000 in today's money) stipend offered by St. Andrew's.

Before they left Adelaide, Mrs. Gardner was presented with an album of photographs of prominent SA citizens and church members taken by the Townsend Duryea studio.

A protracted state of hostility between Gardner and an influential section of the congregation[15] resulted in declining attendance at services with concomitant reduction in collections and pew rents,[16] and after the initial contract period elapsed his stipend was halved.

[21] People of all classes were sorry when he left [Adelaide], and will be gratified if in Victoria his experiences are more pleasant than they have been in Launceston, if, in fact, his lot becomes more like what it was in South Australia.

In him extremes met, and folk who relished his oft scathing style of platform utterances knew that under a rough exterior there was a cordial and kindly nature.