Many students have difficulty learning symbolic and molecular representations of chemistry. This study investigated how students developed an understanding of chemical representations with the aid of a computer-based visualizing tool, eChem, that allowed them to build molecular models and view multiple representations simultaneously. Multiple sources of data were collected with the participation of 71 eleventh graders at a small public high school over a 6-week period. The results of pre- and posttests showed that students' understanding of chemical representations improved substantially (p < .001, effect size = 2.68-. The analysis of video recordings revealed that several features in eChem helped students construct models and translate representations. Students who were highly engaged in discussions while using eChem made referential linkages between visual and conceptual aspects of representations. This in turn may have deepened their understanding of chemical representations and concepts. The findings also suggest that computerized models can serve as a vehicle for students to generate mental images. Finally, students demonstrated their preferences of certain types of representations and did not use all types of three-dimensional models interchangeably. © 2001 John Wiley & Sons, Inc. J Res Sci Teach 38: 821–842, 2001