The roots of what is now known as Harmony Hill United Methodist Church, stretch back centuries. The Harmony Methodist Episcopal Church Stillwater held its first service or “class” in the fields and log cabin of Jacob Main located on Catfish Pond Road which is now known as Middleville Road. Elijah Woolsey, a circuit rider preacher, gave the first sermon to 12 people. In 1832, a church building was erected by Thomas Dildine on 3 tracts of land donated by Dildine, his wife and Peter Wintermute for $1350. A dedication sermon was preached by Isaac Winner, a circuit rider. In 1839, the Harmony Methodist Episcopal Church at Stillwater was designated as an official station and had its first full time pastor. 

In 1854, Swartswood Methodist Episcopal Church was built on land donated by John V. Hankinson, the former clerk, of Stillwater Township for $1750. It shared a pastor with the Harmony Methodist Episcopal Church of Stillwater and the Methodist Episcopal Church in Waterloo Village. In 1865, it was decided that the pastor would preach at Harmony in the morning and Swartswood in the afternoon. In 1873, the bell was bought for $100. In 1888, votes were taken and Swartswood separated from Harmony and had its own pastor and parsonage. In 1920, Swartswood and Harmony reunited and again became one charge, sharing a pastor. In 1923, the time of services in Swartswood were moved to 9:30 AM. In 1927, Harmony Methodist Episcopal Church was renamed the Stillwater Methodist Church. In a yet to be documented year, Swartswood Methodist separated from the Stillwater Methodist church and became a separate charge. In 1944, electricity was added to the Swartswood Church. In 1965, the side annex and bathrooms were added to the Swartswood Church. 

At a joint Annual Conference meeting held in 1974, held at Camp Aldersgate near Swartswood, frustration about “too few hands to do the work”, the limitations imposed by having a shared pastor for two parishes, and the heavy financial burden of running and maintaining two buildings were discussed. A question was asked by a newer member: “Has a merger ever been considered?” “Should one be considered?” As a result, a committee was formed to explore the feasibility of a merger. The committee consisted of Pastor J. Lawrence Brasher, Lay Leader James White of the Stillwater church, Lay Leader, Peter Mahler of the Swartswood Church, Helen Campbell of Swartswood and Marge Finke of Stillwater. Eventually, a consensus was reached, a plan of merger proposed and discussed by each congregation through meetings and home visits. Finally, separate votes were taken in each congregation. When both congregations approved the merger plan, the Annual Conference of the Greater New Jersey United Methodist Church granted the merger. John Knox, Esq. was retained to draw up and execute the legal papers to make the merger official. On June 1, 1975, the last service was held in the Swartswood Church. The reunited congregation held its first joint worship service on June 8th 1975. Because the Church in Stillwater had a fellowship hall, a parsonage and more parking area, it was chosen as the site for Harmony Hill UMC. That name was created to demonstrate that this was not a closure or an absorption of the Swartswood Church, but the merger of two congregations into one new and vital congregation. The name reflected the like-mindedness of the congregation, the historical name of the area on which the church was erected and the original name of the Stillwater church (Harmony Methodist Church). 

At the time of the merger, the Swartswood Church owned a house, the former parsonage, located adjacent to the church. It was sold to the tenant. The money from that sale was used to remodel the kitchen in the fellowship hall in Stillwater. The basement was renovated into Sunday School rooms and the kitchen was moved into the upstairs space adjacent to the fellowship hall.

The former Swartswood Church building was sold for $1.00 to Stillwater Township with the stipulation that the exterior appearance was to be maintained as it was and if the township no longer wanted the property, it was to revert back to Harmony Hill United Methodist Church for $1.00. Initially, several members of the town council, did not want the building. They had wanted to build a new municipal building for approximately $500,000 in Middleville to house the tax collector (who had previously worked out of a chicken coop on a farm in Stillwater), the police department and township offices. When it was pointed out at a public meeting that moving the tax collector, police department and joint municipal court to the Swartswood Church property at little or no cost, many residents commented on the logic of accepting the offer. The township committee voted to accept the offer. When the Stillwater Police Department was disbanded and the municipal court was moved to different venue, the township no longer wanted the building. For $1.00 the property reverted to HHUMC. It was offered to a number of nonprofit organizations within the county. Samaritan Inn was selected by the church to receive the property at no cost. Samaritan Inn moved its headquarters, food pantry and other outreach programs to the property. Sussex County Habitat for Humanity did the work to renovate the sanctuary/municipal court. In 2010, when structural issues with the cupola made it necessary for it to be removed, the bell was saved and moved to an open-air pavilion adjacent to HHUMC. At the 35th Anniversary of the merger, a worship service was held at HHUMC on May 30, 2010 and the bell was rededicated.