The north portal lies in the north of the municipality of Erstfeld at an elevation of , east of the Reuss. There, the tunnel penetrates the western slopes of the Bälmeten and Chli Windgällen (although only marginally) before passing below the valley of the Chärstelenbach, a creek in the Maderanertal. From there, the tunnel runs parallel to the small valley of Etzli, below the Witenalpstock. The main crest of the Glarus Alps, which is the watershed between the Reuss and the Anterior Rhine, is crossed below the Chrüzlistock, the crest having an elevation of about at this point. From the crest and border, the tunnel runs parallel to the small valley of the river Strem (Val Strem) before passing below Sedrun and the Anterior Rhine. From the bottom of the valley, the tunnel proceeds towards the valley of the Rein da Nalps (Val Nalps) and passes east of Lai da Nalps, before crossing the Gannaretsch range below the western summit of Piz Vatgira (). This is the deepest point of the tunnel, with a rock layer of above it. The tunnel then passes below the valley of the Rein da Medel (Val Medel) and west of Lai da Sontga Maria. After a few kilometres the tunnel crosses the watershed between the Anterior Rhine and the Ticino, just north of Pizzo dell'Uomo (). This point corresponds to the main chain of the Alps, and is the main drainage divide between the Rhine and the Po. For a few kilometres, the tunnel passes below two western tributaries of the Brenno in the Valle Santa Maria before crossing the last range, west of the Passo Predèlp (about ) and east of Faido. It then follows the eastern slopes of the large Valle Leventina, the valley of the Ticino, for about to the south portal at Bodio, at an elevation of , just before Biasca, where the Brenno converges with the Ticino.