The history of St. Mary Church dates back to 1894 when a few Catholic families of the community purchased the church property from the Church of Christ for $800.00. This original church was very small but would accommodate the few families in the parish at that time.

On March 26, 1912 St. Mary's Mission was legally incorporated into the Sioux City Diocese under Bishop Phillip Garrigan, the first bishop of the diocese.

Father George Costello, resident past of St. Joseph's in Lohrville, was appointed pastor of St. Mary's Mission. Father Costello drove a buggy from Lohrville every second Sunday of the month. On alternate Sundays, Father Costello took care of his mission in Rockwell City. Occasionally, weather conditions made it impossible for Father to reach Lake City on those Sundays. After a long weary wait, the congregation would recite the rosary and return to their home. Special early Masses were scheduled near the feast of the Nativity and the feast of the Resurrection, in order to provide an opportunity for the parishioners to receive the Sacraments.

In 1929 St. Mary became a mission of St. Mary of Sac City under the Pastorate of Father Daniel Tewell. Later, Father Tewell was replaced by Father Otto Dentlinger.

Under Father Dentlinger's pastorate, the original church was raised, turned to the east and a basement with furnace, kitchen and restroom added. The Sanctuary and Sacristy were added to the west. In 1935, through the determined efforts of Father Dentlinger, the mission, which now numbered about 37 families, was given the status of a parish.

A rectory was purchased on July 13, 1935 and Father Leo Berger was appointed to serve as the first resident pastor. The entire nation was suffering the depths of a depression and on Father
Berger's first Sunday in Lake City the collection basket tallied less than one dollar, which was supposed to buy groceries and take care of any other weekly expenses. After much pinching and struggling and with some much needed help from kindly Bishop Heelan, St. Mary in Lake City managed to survive.

From 1939 to 1955 St. Mary had the following priests serve the parish: Father Reinhard Nemmers, Father Louis Lynch, Father Thomas Lawless, Father Robert Joynt, Father Joseph Roder, Father Clement Knobbe, and Father Louis Anthofer. In 1955 Father James Fandel was appointed to St. Mary and was here until June 1974.

On May 1, 1956 St. Mary purchased two blocks of land in the Westview area of Lake City for $5,000.00. This land was designated as the new site for the future St. Mary parish and specifically purchased to build a new church and rectory. Following 5 years of raising funds for the new church, His Excellency Bishop Mueller suggested that we take definite steps toward starting the building of a new church and rectory. On February 13, 1962, Father Fandel met with the finance committee and the trustees, it was decided that they had enough money to start making necessary plans. Dedication of the new St. Mary Catholic Church and the blessing of the new parish house took place at 11:00 a.m. Tuesday, February 5, 1963.

The exterior design of the new church features the use of maintenance-free materials, including Norman brick and stone trim, aluminum stained glass windows, cement asbestos shingles, copper gutters and flashings. The church faces east with a canopied entrance over which is erected a statue of the Blessed Mother.

The interior was designed to seat approximately 400 people. A large overflow room off the sanctuary is so located that it can also serve as a classroom. This, with a full balcony and first floor cry room, will provide seating for an additional 90 people.

The new rectory is designed to accommodate two priests and includes housekeeper quarters.
Two offices and a full basement, finished for classroom purposes are added features.

Total cost for the new church and rectory was $140,284.00.

With the continued growth of St. Mary facilities for parish activities and catechetical instruction were inadequate, resulting in the construction of a combined Parish Hall and Educational Center. This building was completed and dedicated by His Excellency Bishop Frank H. Greteman in 1970. The newly completed building consists of a large general meeting room and dining area, a fully equipped kitchen, seven classrooms, a priest's office and two bathrooms.

In 1974  Monsignor Joseph Tolan was appointed to St. Mary followed by Father Robert
Fangman. Father Joseph Kerwin came in 1976 and stayed until 1986. At this time St. Mary had 180 families and 175 children in CCD In 1986 Father Dean Walker was assigned followed by Father Robert Thiele.

Due to a shortage of priests, clustering became necessary. Father Dennis Sefcik came to St.
Mary from St. Joseph in Lohrville, thus serving as pastor of both churches.

On May 30, 1998, a major hail storm hit the area and replacement of the roofs and windows were necessary for all three buildings. In August of 2001, the parish paved the parking lot around the parish center.

Father Sefcik remained at St. Mary Catholic Church until July 2003 when he was replaced by Father Timothy Boekelman who was ordained in 1970 and originally from the Algona area. He served the cluster church of Lake City and Lohrville from July 2003 to July 2009. 

Father Lynn Bruch, originally from the Halbur area, came to St. Mary in Auburn, St. Joseph in Lohrville, and St. Mary in Lake City in July 2009. Father Bruch had been with the Webster County cluster of churches.

In December 2014 St. Mary Catholic Church began a "Building Our Future...Preserving Our Past" capital campaign for the reconstruction of the parish center. Construction began in the spring of 2015 and completed in 2016. The new center includes six classrooms, a conference room, two offices and a parish hall with seating for 240.

The parishes of St. Mary, Auburn and St. Joseph, Lohrville moved to oratory status  in July of 2017 and became one with St. Mary, Lake City. The parish of St. Mary, Pomeroy moved to oratory status and merged with St. Thomas, Manson. Our cluster includes St. Thomas, Manson, St. Francis, Rockwell City, and St. Mary Lake City which operates as Calhoun Catholic Parishes. A Pastoral Council was formed with representatives from all parishes involved to oversee and coordinate church activities with the county. 

Father Lynn has remained as Pastor of the Calhoun Catholic Parishes throughout this process. Father Zach Jones, a recently ordained priest, joined the staff for the summer of 2022. In July of 2023, Father Brian Feller came to the parish as an Associate Pastor.