The western terminus of the route is at the intersection with NY 414 near the southern end of Seneca Lake just northeast of Watkins Glen.

Between Whitney Point and Chenango Forks, it runs along the eastern bank of the Tioughnioga River.

From the town of Colesville to the Pennsylvania border, NY 79 runs along the western bank of the Susquehanna River.

The route heads north, climbing the side of the large bluff along the eastern edge of Seneca Lake.

As Mecklenburg Road, it heads eastward through rolling farmland and hills toward the city of Ithaca.

As NY 79 approaches downtown Ithaca, it becomes Hector Street and curves to the northeast, then to the southeast as it descends to Cayuga Lake.

It heads southeastward as Slaterville Road through the towns of Ithaca, Dryden, and Caroline, serving several small communities along the route.

The overlap continues to Whitney Point, a village situated at the confluence of the Tioughnioga and Otselic Rivers.

The route heads onward through the rural towns of Fenton and Colesville, where it meets NY 7.

NY 79 continues along the Susquehanna River to the New York–Pennsylvania border, where the road becomes PA 92 upon crossing the state line.

The only notable deviations are local, for easier grades, including along the "hogback" eskers near Center Lisle, and the westbound climb out of Ithaca as a looping Hector Street in place of the original straight climb from halfway up that street (still visible as a right-of-way).

[7][8] On April 4, 2022, work began to replace the bridge that carries NY 79 over the Chenengo River.