The Canandaigua and Corning Railroad Company was incorporated by a special act of the New York Legislature on May 14, 1845 to build between the two points named, and the Chemung Railroad was incorporated on the same date. The Chemung RR was the first to finish its line, from Horseheads, on the New York and Erie Railroad, to Watkins Glen (then known as Jefferson), on Seneca Lake, in 1850. It was operated as a branchline of the Erie, and accordingly used 6 ft (1,829 mm) broad gauge. On March 8, 1850, another act authorized the Canandaigua & Corning to change its name to the Canandaigua & Elmira and connect with the Chemung RR. It opened a line between the Chemung RR at Jefferson and Canandaigua on September 15, 1851, and was also operated by the Erie. On September 14, 1852, it was renamed the Canandaigua and Elmira Railroad Company.
On January 1, 1853, the Erie ceased to operate the two railroads, and the Chemung RR was run as part of the Canandaigua & Elmira, now an independent operation. On July 1, 1853, the Canandaigua and Niagara Falls Railroad opened between Canandaigua and North Tonawanda. It was also 6 ft (1,829 mm) broad gauge, and was leased by the Canandaigua & Elmira RR, giving it access to the Niagara Falls Suspension Bridge.
The Canandaigua & Elmira RR was sold at foreclosure on April 23, 1857 to George B. Holmes and reorganized on May 2, 1857 as the Elmira, Canandaigua and Niagara Falls Rail Road Company, continuing to operate the Chemung RR. On November 6, 1857, the Canandaigua & Niagara Falls RR was also sold under foreclosure. The Elmira, Canandaigua & Niagara Falls RR went bankrupt, and a receiver was appointed on July 1, 1858, the Chemung RR reverting to Erie operation. The bankrupt railroad was sold at foreclosure on July 23, 1858 to Charles Congdon and Robert B. Potter. On August 25, 1858, the foreclosed Canandaigua and Niagara Falls RR was reorganized as the Niagara Bridge and Canandaigua Railroad, which was leased to the New York Central on September 1, 1858. It was regauged to 4 ft 8+1⁄2 in (1,435 mm) standard gauge, depriving the Erie of a broad gauge connection to Niagara Falls. The foreclosed Elmira, Canandaigua and Niagara Falls RR was reorganized on February 18, 1859 as the Elmira, Jefferson and Canandaigua Railroad Company. The Erie continued to operate the Elmira, Jefferson & Canandaigua RR, which in turn operated the Chemung RR, until January 19, 1866. The two lines were then leased to the Northern Central Railway, to replace an unsatisfactory joint routing over the Buffalo, New York and Erie Railroad, the line to be given a third (standard gauge) rail by May 1, when the lease was to take effect.