The AER was built through at least five different geological features.  The city of Sudbury, the northern terminus is perched on the south side of a major prehistoric meteorite impact crater.  From a relatively flat area in downtown Sudbury the railway heads more or less east through the Precambrian Shield.  The route chosen by the road's builders skirts the southern rim of the remnants of the impact crater.  The major nickel, gold and copper mineral occurrences formed by this crater are scattered along the rim  For the most part the builders avoided expensive rock cuts preferring to go around the obstacles rather than through them.  Around Turbine, the roadbed runs through an anomaly in northern Ontario, a flat level valley.  At one time this area was an agricultural centre although now many of the farms have been abandoned.  Continuing east the railway follows a level course along the banks of the Spanish River which it crosses twice before reaching Espanola.

From Espanola the railway turns south and is almost immediately in the midst of the LaCloche Mountains.  These pink quartzite dominated hills are the remnant of an extremely old mountain range that was once much higher.  Rock cuts here are almost unavoidable, but the scenery is beautiful as the railway curves almost continually to avoid mountains and lakes.

Coming out of the LaCloche mountains south of McGregor Bay the railway crosses the the flat limestone plain of Goat Island.  Turner, at the southern end of Goat Island was the site of a major marine shipping dock and yard facilities.  Finally the line crosses the North Channel between Goat and Manitoulin Islands to the town of Little Current.