Processing of multiple representations in multimedia learning environments is considered to help learners obtain a more complete overview of the domain and gain deeper knowledge. This is based on the idea that relating and translating different representations leads to reflection beyond the boundaries and details of the separate representations. To achieve this, the design of a learning environment should support learners in adequately processing multiple representations. In this study, we compared a scientific inquiry learning environment providing instructional support with directive self-explanation prompts to relate and translate between representations with a scientific inquiry learning environment providing instructional support with general self-explanation prompts. Learners who received the directive prompts outperformed the learners who received general prompts on test items assessing domain knowledge. These positive results did not stretch to transfer items and items measuring learners' capabilities to relate and translate representations in general. The results suggest that learner support should promote the active relation of representations and translation between them to foster domain knowledge, and that other forms of support (e.g. extended training) might be necessary to make learners more expert processors of multiple representations.