The trail starts on the west bank of the Hudson River in Albany's Corning Preserve, and travels northward alongside Interstate 787 to Watervliet.

From there, an on-road bike route connects through Watervliet, Green Island and Cohoes to the Mohawk River section.

The trail continues west from Cohoes along the Mohawk River with occasional on-road segments, connecting the communities of Colonie, Niskayuna, Schenectady, Pattersonville, Amsterdam, Fultonville, Canajoharie, Fort Plain, Little Falls, Mohawk, and Ilion before ending in Frankfort.

Many of the pre-existing gaps were filled by the end of 2020 as part of the Empire State Trail project.

It is generally regarded as the Capital District's premier linear park, and is by far the most heavily used, based on a 2016 survey of trail users.