This mixed-method study investigates the effects of interactivity in animations of a molecular-level process and explores perceptions about the animated learning tool used. Treatments were based on principles of cognitive psychology designed to study the main effects of treatment and spatial ability and their interaction. Results with students (n = 189) showed that science majors scored higher than non-science majors in retention measures (i.e., structure and function) but not in transfer. Significant main effects were found for treatment in function questions and spatial ability in structure questions. There was a significant interaction between treatment and spatial ability in structure questions. Additionally, in this study participants believed the key and the motion of ions and molecules were the most helpful parts of the animation. This study shows that students perceive the animations as being supportive of their learning, suggesting that animations do have a role in science classrooms.