In February 1901, a group of Poverty Flat, Idaho, farmers met and pledged to build a canal system to improve local agriculture. Through the efforts of these farmers, a local organization named the Oneida Canal Company Limited emerged, but within a year it underwent a reorganization which resulted in the Oneida Irrigation District (OID). In 1920 the internal workings of the company underwent a second reorganization, and then it was subsequently known at the Twin Lakes Canal Company (TLCC). Over the course of the company's history, management passed from the hands of the local founding farmers to officers that transformed the company into a major organization.

After the canal company was organized, work began on a canal that aimed to pull water from Mink Creek Canyon and direct it to the area near present day Weston, Clifton, and Dayton in Franklin County, Idaho. The construction of this canal eventually transformed the area's agricultural systems by providing roughly 13,000 acres of dry land with irrigated water. Internal bickering and bitterness, however, marred much of company's early history. In 1908, allegations of mishandling district funds were leveled against A. D. Henderson (the first president of the canal company), A. W. Hart (secretary), and George C. Parkinson (treasurer). Litigation dragged on for five years until Judge Henry Rolapp and auditor Orson P. Rumel cleared all three men of the charges.

Due to dissension and mismanagement of the canal district, it fell into financial difficulties and canal construction lagged due to the lack of funds. In 1916 the Amalgamated Sugar Company bought interest in the irrigation district in hopes of improving beet production. The Amalgamated Sugar Company assumed the debts of the canal company and, for a short time, the company was known as the Oneida District of the Amalgamated Sugar Company. Although years behind schedule, the canal was finished largely because of the Amalgamated Sugar Company's money. While the sugar company continued to own a substantial percentage of the canal company's stock, its control only lasted until the 1920s, whereafter ownership passed back to the TLCC. However, from the completion of the canal to the present, the TLCC has functioned to aid southern Idaho's agricultural economy.