The Waterville Baptist Church is one of the oldest churches in Central New York. It was originally named the First Baptist Church of Sangerfield. Meetings were held in private homes in the fall and winter of 1797. On April 14, 1798, 8 people met in the home of White Osborn in Sangerfield, to discuss the possibility of beginning organized services. Their concern was "to consider what measures were best under present circumstances to keep up the public worship of God." The decision was made to move forward.

The earliest organized services were held in the home of Benjamin White, the first settler in Waterville. His home was located on the site of the present Post Office and Home Shoppe. On December 10, 1798, 17 members accepted the proposed Articles of Faith and Church Covenant and the church "officially" began.

In December 19, 1798, ministers and members from churches in Fairfield, Whitesboro, Paris, and Hamilton met to examine the church's Articles of Faith and Covenant. They were approved, and the church was given the "right hand of fellowship." At this same meeting, Joel Butler was given charge of the church, as its first pastor. He continued to serve as pastor until 1805.

The first church building was erected in 1800. The 40' x 50' building cost $400, and was paid for in produce. It was located slightly northeast of the present building. An interesting historical connection with the church, is that the steeple was completed the day Waterville residents heard that the War of 1812 had ended. To mark the occasion, a sailor climbed the steeple and placed a burning candle at the top.

The present building was constructed in 1832. The property was donated to the church by Benjamin White in 1803. The portion of land donated included the entire "flat-iron tract" in the center of Waterville. 10,000 bricks from the Waterville area were used in the building. Around 1872, a foyer was added to the front of the building, as well as structural changes made to the steeple. Due to repeated lightning strikes, the main part of the steeple was removed in 1948. The bell tower and clock needed to be removed in 1981.