This study investigated the effectiveness of multiple scaffolding tools in helping students understand a complex problem. In order to support students with this task, a multimedia learning environment was developed based on the cognitive flexibility theory (CFT) and scaffolding through computer-based tools. Seventy-nine 10th-grade students in an urban high school participated in this study. A quasi-experimental method was used to compare the effectiveness of different scaffolding tools within this learning environment. Scaffolding used in conjunction with CFT principles did not affect students' ability to consider multiple perspectives or their numbers of misconceptions. On the other hand, scaffolding tools had varying effects on students' problem understanding, and a significant interaction was found between the different scaffolding tools used. This study raised questions about the effectiveness of combining multiple scaffolding tools within a multimedia environment. (Contains 6 tables and 3 figures.)