Anglican services began in a cart shed which belonged to Mr Fitzgibbon. A reserve of 1¼ acres was set aside for Church of England purposes in 1859 and the first church building erected at that time. Mr Rodda performed the duties at that time. The Church of England building was used by other denominations until they had buildings of their own.

In an 1871 survey, Anglican parisheners in the Shire numbered 481. The first Anglican service at Little River was held in August 1857 and Rev Frederick Strickland was appointed to the Parish of Station Peak (Little River and Werribee) in 1864.

In 1886 the district was divided and Rev H. Kelly came to Lara whilst Rev Alfred Caffin continued in what was now the Reader's District of Wyndham, until the Stipendary Reader F.W. Ellis arrived from Omeo in 1887. In 1891, the then reader, Henry F. Miller was ordained and became Curate in charge of the new Parochial District of Werribee.

The foundation stone of the new red brick church was laid by John Percy Chirnside, M.P. on 24 October 1900. After his death, his widow Ethel, presented a two panelled window to the church in his memory and one in memory of their daughter Molly (Ethel Charlton). Other stained glass windows in the church honour early pioneers of the district.

The Rev. Andrew Hanna was inducted to the pastoral charge of the Presbyterian congregations of Wyndham, Little River and Duck Ponds (Lara) in 1866. Werribee services were held on Sunday afternoons in the Church of England building. Mr Hanna held the charge for only a short time for soon afterwards he resigned from the ministry.

About this time the first manse was built a mile out of town. Rev J. Lambie was inducted in March 1868 accepting a call signed by 20 members. He remained until 1881. In 1871 a survey showed that there were 185 adherents of the Presbyterian Church in Werribee.

In 1883 the Rev William White was invited from Scotland mainly through the interest of Thomas Chirnside. Chirnside laid the foundation stone of the bluestone church in Werribee in February 1884 and paid for the erection of the church and manse, both of which were built on his land. In the same year the foundation stone for the Little River Church was laid by Mrs White, wife of the Werribee minister. Land for this church was donated by Paul Cameron who also gave money and building materials for the erection of the church. The original bluestone building still stands.

The land on which the Werribee church was built was subdivided and made over to the Trustees of the Church in 1902. The church had stained glass windows presented by the Chirnsides and a carved oak pew which had been raised and enlarged to hold the choir.

In 1895 Rev John McIntosh, Minister of the Werribee church began holding services fortnightly at the Truganina Baptist Church. In 1907 he bought the Baptist Church building for use by the Presbyterian Church.

The first Methodist/Wesleyan services in the area were conducted by Sam Hayes, school teacher at Truganina. In the late 1850's a bluestone Methodist Church was built on the bank of Skeleton Creek, Truganina. A wedding was held there in 1861. For a few years, the building was used as a school, until a school was built in 1869. The building was later sold and the stone used to build the Robinson house in Truganina.

A Methodist Church existed in Mount Cottrell as early as 1866.

In Werribee, township land was reserved for a primitive Methodist Church in 1869 and trustees were appointed in 1872. Figures for Church adherents in 1871 show 83 Methodists in the Shire. The first records of congregation in Werribee date from 1895 when Rev H.M. Jennison began services in the old Shire Hall. The congregation gradually diminished and boys from Wesley College came to conduct meetings in the streets and in the Old Shire Hall. As a result of this, the Rev A. Doran was appointed to the circuit with a congregation of 13. A wooden church was built in 1899 and 280 people attended the first service in a building designed to seat 200.

A Baptist Church building of corrugated iron was erected in Truganina in 1862 on land donated by Samuel Evans. A local preacher, John Cropley from Rockbank used to travel across the country to take services at Truganina. From 1862 Rev William Wade the first minister came once a month from Footscray to preach.

The number of Baptists recorded in the Shire in 1871 was 37. Over the years attendance diminished and the building was bought by the Presbyterian minister from Werribee. It was burnt down in the bushfires of 1969.

In 1857 Bishop Goold established the new parish of St Michael's Little River. At the time there were very few Catholics living in the vicinity but a small bluestone church with a slate roof was erected on reserved land adjoining the present Little River Railway Station.

The Rev Father Ronald Rankin, the first Scottish Highland priest in Victoria, was in charge of the parish, and Mass was celebrated every Sunday. A Denominational School was held in the building for some years, then a wooden school was ereccted in the grounds.

When Fr. Rankin died the parish was closed because of a shortage of priests and Mass was celebrated once every six weeks by priests from Geelong. As the population of the area grew, so did the size of the congregation and the little church was extended and renovated. Patrick Preston, proprietor of the Rothwell Inn had a bell cast in Dublin and erected near the Church. In 1906 Werribee and Little River which had been in a combined parish with Williamstown were made a separate parish under Rev. Fr. Heaney.

The bluestone church was demolished in 1922 and some of the stone was used in the foundations of the new brick church which was opened the same year.

Land for a Catholic Church in Werribee was reserved in 1861 and again in 1868. With the encouragement of Fr Thomas Neville and Fr James McGillicuddy a Building Committee was formed. Cr Kelly applied on its behalf for permission to quarry bluestone at the Council quarry for the building of the Church, and this was granted. The church was completed and was blessed and opened by Rt Rev J.A. Goold Bishop of Melbourne in 1871. The predominance of Scots in the parish influenced the naming for the patron saint of Scotland - St Andrew. The building still stands in the grounds of St Andrew's.

The body of the present brick church with a temporary sanctuary was built in 1898 at the instigation of Fr Gerald Byrne of Williamstown. In 1937-8 the church, presbytery and garden were renovated and the present sanctuary and two transepts were added. These additions were blessed by the Most Rev Daniel Mannix, D.D., Archbishop of Melbourne in 1938. Further alterations were made to the building in 1980.

In 1911 a convent was built opposite the church for the Sisters of Saint Joseph who had come to the parish in 1910. This convent was replaced in 1971.

Although 52 people were listed as adherents of the Independent Church in the Shire in 1871, there is no record of an Independent Church meeting in Werribee, although there was one in Little River. One of the earliest travellers to record his experiences here was an Independent Minister Rev William Waterfield who had been pastor of the Church of Christ in Wrexham, North Wales and came to Australia as a representative of the Colonial Missionary Society in 1836.

Waterfield remained in Melbourne for five years in which time Melbourne's first permanent place of worship was opened under his charge on the site of the present Independent Church in Collins Street.