Multi-User Virtual Environments (MUVEs) provide a rich and immersive context for introducing inquiry-based and Problem-Based Learning (PBL) into science classrooms. MUVES can have a significant effect on learning outcomes, however, illuminating how particular design features interact with those outcomes is an important area of investigation for the field. There has been a trend in the development of instructional technology towards designing MUVEs with a top-down, central narrative and positioning the student as an active protagonist in the storyline. A case study contrasted two MUVEs focused on the same science content, a eutrophication scenario, but with different overarching structures and types of guidance. Quest Atlantis: Mystery of Taiga River adopts a narrative approach in which students enter into the storyline about a declining fish population in a local national park and develop an explanation for who is responsible. EcoXPT adopts an epistemological approach that seeks to leverage the affordances of MUVEs to engage students in the investigative approaches that ecosystems scientists use; it invites students to explore an ecosystem in which they discover an environmental puzzle and then, using epistemologically authentic approaches, try to figure out what is going on and why. The case study found that these contrasting structural features interacted with student modes of engagement and their learning outcomes, with the Taiga classes grasping complex human impacts on the environment and EcoXPT classes understanding the epistemologies involved in understanding complex processes within ecosystems.