In order to understand water balance in plants, students must understand the relation between external representations at the macroscopic, microscopic, and submicroscopic levels. This study investigated how Slovenian students (N = 79) at the primary, secondary, and undergraduate tertiary levels understand water balance in plants. The science problem consisted of a text describing the setting, visualizations of the process occurring in a wilted plant stem, and five tasks. To determine students’ visual attention to the various elements of the tasks, we used eye tracking and focused on the total fixation duration in particular areas of interest. As expected, primary school students showed less knowledge and understanding of the process than the secondary school and university students did. Students with correct answers spent less time observing the biological phenomena displayed at the macroscopic and submicroscopic levels than those with incorrect answers, and more often provided responses that combined the macro-, micro-, and submicroscopic levels of thought. Learning about difficult scientific topics, such as the water balance in plants, with representations at the macroscopic and submicroscopic levels can be either helpful or confusing for learners, depending on their expertise in using multiple external representations, which is important to consider in biology and science education.