This work describes the modeling of a hypermedia learning system (called “Biomec”) that integrates physical, biomechanical and anatomical concepts involved in the human motion and a study carried out with undergraduate students who interacted with the system. The instructional design of the “Biomec” hypermedia system was developed on the basis of a theoretical framework which articulates the Cognitive Flexibility Theory and the interdisciplinary approach to knowledge. The system was evaluated based on its use by students of Biomechanics I and Kinesiology in a Pre Service Teachers Training Course of Physical Education aiming to discuss the following questions: (i) what is its impact on the students’ attitude related to Physics? (ii) in what extent does the hypertextual approach to the content favor the interdisciplinary conception of human motion? (iii) in what extent do the students’ navigation profiles adapt to conceptual needs of the different disciplines of the course? The students answered instruments that assessed affective and cognitive aspects before and after the interaction with the system, and had their navigation registered and analyzed. The set of data obtained allowed to conclude that the “Biomec” system is a relevant instructional material, capable of positively influence the students’ attitude related to Physics, to favor the interdisciplinary approach of human motion and to attend the students enrolled in Biomechanics I better than the students enrolled in Kinesiology.