From the crossovers and junction at Hoffmans, SS-11 ("NA"), with tower between the two pairs of tracks, a signal bridge overhead and a road alongside to the north, where 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, and the double track passenger line, with a single track freight line alongside to the north, continues east-southeast, past two dirt road grade crossings, the rail bridge overhead (above), the river alongside to the south, and a road bridge overhead, where the line turns southeast, past two grade crossings, a road bridge overhead, , a grade crossing, , a B&M rail bridge overhead, three grade crossings, track pans and water columns at Scotia (MP 161.3), where there is a yard on the north side, a connection to the Delaware & Hudson curves north-northeast, the freight line doubles, and the main line turns south, a road bridge overhead, MP 161, a former rail bridge overhead, and a road bridge overhead, a through girder bridge across the Mohawk River, two bridges over roads, a through truss bridge over a road, the NYC Troy branch trails in from the northeast, a through truss bridge over a river and a through girder bridge over a road, the island platform with an umbrella shed on the elevated line for the passenger station (with depot and parking lot below on the south side) at Schenectady (MP 159.8), and crossovers at SS-8 ("SC"), where the D&H leaves on the east side before descending and passing below. There is a road bridge overhead, a bridge over a street, and the General Electric plant is close by on the west side of the line, followed by a bridge over a street and a road bridge overhead.
The line curves southeast, past a road bridge overhead, and passes beneath the Carman Branch, which then descends to join on the north side at the crossovers at SS-7 ("AS"), where the second freight track ends, passing three road bridges overhead, two grade crossings, a small yard on the north side at Karner, a road bridge overhead, a grade crossing, a short siding on the north side, the shops and yard at West Albany (where the passenger line southeast to Albany Union Station continues straight ahead (on the south side), and the freight line turns east-southeast, past a through girder bridge over a street, a road bridge overhead, a wide road bridge overhead, 6-8 yard tracks on the north side, a road bridge overhead, a bridge over a stream, Rock Cut (MP 145.2), a road bridge overhead, a through girder bridge over a street, a through truss bridge over a street, a connector to the D&H heading away on the south side, a through girder bridge over the D&H.
There are two bridges over streets, a bridge over a road on the west bank of the Hudson, and the multi-span through truss bridge over the Hudson River with the movable span at the west end, crossovers at SS-D, tower on the south side, on the east side of the bridge, where the Troy line trails in from the north at a wye and the main line turns south, past crossovers at SS-100, where three tracks start, with the tower between two of them, an angled road bridge overhead, and the passenger tracks from Albany rejoin from the west and the Boston & Albany tracks to the east continue on the east side, an additional pair of passenger tracks on the east side start at the north end of the station at Rensselaer (MP142.1), where there is a road bridge above the platforms. There are crossovers at SS-98 at the south end of the platforms