Navigated instrument guide systems and related methods can identify an absolute position of an instrument received within an instrument mount of a robotic arm. A navigation array unit of the guide system can include a main array and a mounted array. The main array can identify a position of the robotic arm and the instrument mount, while the mounted array can identify a depth position of a distal end of an instrument received within the instrument mount. The instrument can be passed through a lumen of the mounted array as the instrument is inserted into the instrument mount. The mounted array can be configured to translate relative to the instrument mount and the main array with distal translation of the instrument. In this manner, a position of the mounted array can identify a depth position of the instrument without a mechanical connection between the mounted array and the instrument.