Schuyler and Tompkins counties

NY 79 begins at an intersection with NY 414 just north of the Watkins Glen village limits in the Schuyler County town of Hector. The route heads north, climbing the side of the large bluff along the eastern edge of Seneca Lake. At the top of the hill, NY 79 enters the village of Burdett as Main Street. As it passes through the village, NY 79 turns eastward as Lake Avenue. East of Burdett, the route passes through the hamlet of Bennettsburg prior to intersecting NY 227. While NY 227 heads north to serve Reynoldsville, NY 79 continues east to Mecklenburg, the site of its junction with NY 228.

East of Mecklenburg, NY 79 passes into Tompkins County and the town of Enfield. As Mecklenburg Road, it heads eastward through rolling farmland and hills toward the city of Ithaca. It intersects NY 327 at Enfield Corners in this stretch. 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. At the base of the hill, the route crosses the Cayuga Inlet and enters downtown, where it splits into a one-way couplet along State Street (eastbound) and Seneca Street (westbound). NY 79 eastbound shifts one block south at Fulton Street (NY 13, NY 34, and NY 96 southbound) to use Green Street. The one-way couplet ends one block east of Aurora Street at the "Tuning Fork" as Green and Seneca streets merge into East State Street, recently double-named Martin Luther King Jr. Street. NY 79 follows State Street southeastward through eastern Ithaca into the town of Ithaca. The portions of NY 79 between the Ithaca west city line and NY 13A, between NY 89/96 and Meadow Street (NY 13/34/96 northbound) and between Green Street and the Ithaca east city line are maintained by the city.

The portion of NY 79 east of the city limits is markedly more rural. It heads southeastward as Slaterville Road through the towns of Ithaca, Dryden, and Caroline, serving several small communities along the route. NY 79 crosses into Tioga County upon passing over the west branch of Owego Creek.

Tioga, Broome, and Chenango counties

NY 79 heading southbound through Windsor from the intersection with Broome CR 16

NY 79's stay in Tioga County is wholly confined to the town of Richford. The routing of NY 79 in Richford is hilly and heavily rural, with the one exception being at NY 79's junction with NY 38 in the hamlet of Richford. The route heads into Broome County, where it meets U.S. Route 11 (US 11) in the town of Lisle just east of the Lisle village limits. NY 79 joins US 11 southward along the Tioughnioga River to a partial interchange with I-81 at exit 8. The overlap continues to Whitney Point, a village situated at the confluence of the Tioughnioga and Otselic Rivers. In the village, NY 79 leaves US 11 in favor of a short overlap with NY 26 across the Tioughnioga River. On the opposite bank, NY 26 and NY 79 split at a junction that also features NY 206.

South of Whitney Point, NY 79 continues southeast along the Tioughnioga River to the vicinity of Chenango Forks, where it intersects NY 12. It briefly joins NY 12 along the banks of the Chenango River, then crosses the river and enters the town of Fenton. About 3 miles (5 km), NY 79 veers into Chenango County for just under 1 mile (1.6 km) before reentering Broome County. The route heads onward through the rural towns of Fenton and Colesville, where it meets NY 7. NY 79 runs concurrent with NY 7 to Harpursville. Here, NY 79 turns southeast and connects to I-88. Past I-88, the route follows the western bank of the Susquehanna River southward through Ouaquaga, once a large Iroquois village which was destroyed by the Continental Army in 1778, to the village of Windsor. Inside the village, NY 79 meets NY 17 at an interchange that is also the temporary eastern terminus of I-86's eastern segment. NY 79 continues along the Susquehanna River to the New York–Pennsylvania border, where the road becomes PA 92 upon crossing the state line.