Usually, students learn more if the method of instruction matches their learning style. Since Physics and Chemistry deal with three–dimensional (3–D) objects, the ability to visualize and mentally manipulate shapes is very helpful in their learning. In fact, much of what Physics and Chemistry students know takes the form of images. However, little attention has been given to the pedagogical effectiveness of visual stimuli in those disciplines. Computers are being increasingly used as teaching tools. The new approaches include simulations, multimedia presentations and, more recently, virtual environments. Computer–based worlds are useful to visualize physical and chemical processes allowing for better conceptual understanding. Since 3–D virtual environments need to be explored and evaluated in science education, we have created a virtual environment (Virtual Water) for studying phases of matter, phase transitions and atomic orbitals at the final year of high school and first year of university levels. Based on that work, we discuss the implications of visual learning in designing strategies to cater for differences in learning modes. Our study indicates that 3–D virtual environments may help students with high spatial aptitude to acquire better conceptual understandings. However, only some parameters (interactivity, navigation and 3–D perception) have shown to be relevant and only for some topics. On the other hand, stereoscopic visualizations do not seem to be relevant, with the exception of crystalline structures.