Inquiry learning is an educational approach in which learners actively construct knowledge and in which performing investigations and conducting experiments is central. To support learners in designing informative experiments we created a scaffold, the Experiment Design Tool (EDT), that provided learners with a step-by-step structure to select variables and to assign values to these variables, together with offering built-in heuristics for experiment design. To further structure the students' approach, the EDT was offered within a set of detailed research questions which again were grouped under a set of broader research questions. Learning results for learners who worked with the EDT were compared to results for learners in two control conditions. In the first control condition, learners received only the detailed research questions and not the EDT; in the second control condition, learners received only the limited set of general research questions. In all conditions, learners conducted their experiments in an online learning environment about the physics topic of Archimedes' principle. Conceptual knowledge was measured before and after the intervention using parallel forms of a knowledge test. Overall results showed significant learning gains in all three conditions, but no significant differences between conditions. However, learners who started with low prior knowledge showed a significantly higher learning gain in the EDT condition than in the two control conditions. This result indicates that the effect of providing learners with scaffolds does not follow a "one-size-fits-all" principle, but may depend on specific learner characteristics, such as prior knowledge.