The perception of visual information is essential in satisfactory control tracking performance. Modern interface technologies such as stereoscopic three-dimensional displays allow for a more ecological representation of three-dimensional surroundings in a remote teleoperative environment without natural binocular vision. However, the effects such interfaces have on current human controller models are unknown yet desired from a cybernetic perspective. This paper presents the work to identify and quantify manual control behavior in depth control tracking tasks with stereoscopic vision. A human-in-the-loop experiment was conducted in two different environments with twenty four participants of which sixteen were inexperienced stereoscopic display users and eight were frequent users. Four different display conditions were tested; a baseline flat-plane view and three depth views with varying stereopsis. The change of predominantly studied flat-plane control tasks to depth tracking tasks with the considered stereoscopic display settings was found to strongly affect human capability to perform control tasks. The control-theoretic approach to identify and quantify manual control behavior in depth tracking tasks helps to extend current knowledge by integration of human behavior and adaption to modern system’s three-dimensional interfaces.