Halswell was one of the earliest areas of settlement in the Christchurch region. Initially part of the Upper Heathcote Parish (which included Riccarton, Halswell, Templeton and Governor's Bay), it became part of the parochial district of St Peter's, Riccarton about 1857. Land had apparently been set aside - probably by the Canterbury Association - for 'St Mary's on the Halswell' by this time.

Rev. Croasdaile Bowen (1831-90), second son of C. C. Bowen, Speaker of the Provincial Council, was ordained in 1857, and became first a curate and later vicar (in 1859) of the parish of St Peter's. He soon became a familiar figure in Halswell, galloping across the countryside after morning services at St Peter's to take a service at the Halswell schoolroom. With the population of Halswell increasing; and an edict in 1857 from H. J. C. Harper, the newly ordained Bishop of Christ Church, that every settlement should have its own church as soon as possible, Bowen was anxious that a church be constructed there. Tenders for a stone church were advertised in 1861. Prominent architectural firm Mountfort and Luck submitted plans, but these proved too expensive to build, and the church was redesigned in timber, with capacity for future enlargement. Tenders for construction were called in May 1862, and the foundation stone laid in March 1863. The 120-seat church was completed by builders Raistrick and Sons at a cost of £650, and opened by Bishop Harper on 4 November 1863. On 24 July 1865, the Halswell church site was granted by the Crown under the Public Works Act (1854) to the Superintendent of the Province of Canterbury, to be held in trust for the Church of England. Three years later, on 23 December 1868, the Superintendent conveyed the site to the Anglican Church Property Trustees. St Mary's and its burial ground were not however consecrated until 19 October 1871, when the church became debt free. A bell, gifted by 'friends at home', was installed in the belfry in 1869. As one of the earliest Anglican churches in the Canterbury settlement, St Mary's was presented with one of the four sets of altar plate sent from England by the Canterbury Association.

Benjamin Mountfort (1825-1898) was born in Birmingham, and articled to pioneering Gothic Revivalist Richard Carpenter in London for four years. After a short period practising in Britain, Mountfort emigrated to Canterbury with his family aboard the Charlotte Jane in 1850. After initial setbacks, he established himself as one of New Zealand's leading architects, and the most talented and individual practitioner of Neo Gothic in the country. Appointed Provincial Architect in 1856, Mountfort was also frequently employed as an ecclesiastical architect. Consequently many prominent public buildings in Canterbury, constructed over a forty year period, bear his distinctive stamp. Some of the designs for which he was responsible include the Canterbury Provincial Government Buildings (1858-65, Cat I), Canterbury College (1875-96, Cat I) and Canterbury Museum (1869-82, Cat I). With building activity growing and the imminent prospect of work for the Provincial Government, Mountfort entered into partnership with his sister's husband, Issac Luck, in 1857.

Issac Luck (1817-81) arrived at Lyttelton in 1851, and soon afterwards advertised his services as 'builder, architect and surveyor'. Two years later he married Susanna Mountfort. As a skilled practical builder rather than a qualified professional architect, Luck probably handled the practical side of business within the partnership, whilst Mountfort was primarily the designer. Luck was a large and hearty man, the antithesis of Mountfort, but the two men seemed to have complemented each other well, and the partnership lasted eight productive years before being dissolved in July 1864.

St Mary's was part of Bowen's Riccarton Parish until 1876, then united variously with Templeton and Addington before being reunited with Riccarton in 1895. In 1898 the church became part of a new Halswell Parish, which also included Tai Tapu, Greenpark and later Spreydon. This parish's first vicar, Rev. Henry Williams, also served as chaplain of Sunnyside Asylum. Since 1957 the parish has encompassed St Mary's, and All Saints Church, Prebbleton.

During 1890-1 St Mary's underwent a major extension and refurbishment at a cost of £350 by Addington builder H. Topliss, overseen by architect R. W. England. Initially a south transept was added to the church, forming a chamber to house an organ acquired in 1882. Following this, fifteen new cathedral-glass leadlight windows from the London firm of Taylor and Oakley were installed, the altar furniture replaced, the roof reshingled - with the addition of new crestings and filial crosses, the interior and exterior repainted, and a lych gate built. The church was then reopened by Harper's successor, Bishop Julius, in March 1891.

Robert William England (1864-1908) was born in Lyttelton, the son of Robert West England, a partner in the construction firm, England Bros. At the age of nineteen he went to England to study architecture, and was articled to Joseph Lancaster Ball of Birmingham for three years. In 1885 England was admitted to the Royal Institute of British Architects, and returned to New Zealand to set up in practise the following year. In 1906, he entered into partnership with his younger brother Edward Herbert England, establishing a new architectural firm of 'England Bros.'. England was a prolific architect, specialising in large domestic buildings. Prominent dwellings he designed include Holly Lea (the McLean Mansion, 1902, Cat. I), Fitzroy, (now the Nurse Maude Association Building, 1898, Cat. II), and Wharetiki (1902, Cat. II). In 1908 England died following a nervous breakdown.

A three light stained glass window was installed above the altar in 1957 as a gift from Eileen Fairbairn in memory of her family. The Arts-and-Crafts style window, made in England by German-trained artist Joseph Nuttgens depicts Christ in Majesty. The same year, the roof was reshingled and the belfry repaired and strengthened. In 1963 the church was painted and the sanctuary refurbished in preparation for its centenary, which was celebrated that November. The following year the shingles on the roof were apparently again replaced.

Then in 1967 a disastrous fire, believed to have been started by children playing in the vestry, severely damaged the sanctuary, vestry and organ chamber. Although the stained glass window above the altar was damaged, both it and the church's altar plate were saved. Despite initial opinions suggesting that the building could not be salvaged, the decision was made to have the majority of the nave of the old church restored. A new sanctuary and transept to a design of Don Donnithorne were added in Halswell Stone in 1968, at a cost of $16, 738. This doubled the capacity of the church, from 100 to 200. The entire building was re-roofed with decramastic tiles at this time. Donnithorne also prepared plans for the rebuilding of the nave, but these fortunately were never implemented. The composite church was completed by builder John Harris, and reconsecrated by Bishop Pyatt in March 1969. In 1983 a tornado damaged the church's windows. A roof, to a design of Don Donnithorne, was added to the south door of his 1968 addition in 1993. During 2002 the belfry, buttresses and floor were repaired.

The 1882 pipe organ was badly damaged by the fire in 1967. It was replaced by a small Continuo organ from the Calvary Hospital Chapel in 1968, which was in turn replaced with a war memorial organ, gifted by the closing Tai Tapu Methodist Church in 1990.