From the crossovers and junction at CP 169 (MP 169.9), with a signal bridge overhead and a road alongside to the north, where the passenger line, now single track, continues east-southeast, the two-track Selkirk Branch, used by most freight trains heading for Selkirk Yard, departs on the north side, climbing and bridging overhead on a through girder bridge to head to the southeast, Two Main Tracks, Rule 261, maximum speed 40 mph, past a bridge over the Mohawk River, the flat crossing with the West Shore Industrial Track/former Boston & Maine line to Mechanicville, and crossover, at Rotterdam Junction/CP-RJ (MP 39.5), a turn to the south, detectors at South Schenectady (MP 33.6), extra track on the north and south sides at Burdick Road (MP 32.9), a bridge over the Delaware & Hudson main line, the junction with the Carman Branch, on the north side, and crossovers at South Schenectady/CP-SH (MP 31.6), the natural crossover (one track bridging over the other) at Fullers (MP 27.4), a turn south-southeast and then south again, and a spur on the south side at Guilderland Center (MP 25.8), where the line turns south-southeast.
There are crossovers, a flat crossing, and junction (all 30 mph speed restrictions) with the Delaware & Hudson Albany branch at Voorheesville/CP-VO (MP 22.2), where the line turns southeast, New Scotland, CP Unionville-SS (MP 18.0), where Track 5 starts on the north side, current-of-traffic (Rule 251) westbound, and the maximum speed on all tracks drops to 30 mph, the end of Track 5 (into the yard) at MP 17.1), crossovers, the end of double track, start of Track 11 (Rule 261) on the south side, and the west end of Selkirk Yard, at CP-FB (MP 16.9), the end of Track 11 (into the yard) at MP 14.5, Selkirk Yard (MP 14.0), the start (at the yard) of the Inbound Track (Rule 261) at MP 13.7, and the east end of Selkirk Yard, end of the Inbound Track, and the junctions with the Albany Secondary, to the north, and River Line, to the south, at Selkirk Junction/CP-SK (MP 11.5).