This study describes high school students' conceptual development of the basic astronomical phenomena during real-time interactions with a Virtual Solar System (VSS). The VSS is a non-immersive virtual environment which has a dynamic frame of reference that can be altered by the user. Ten 10th grade students were given tasks containing a set of observe-explain questions without mentoring. The findings showed that all participants used the VSS as a visual thinking tool and developed a scientific understanding of the causes of the day-night phenomena. However, alternative dynamic misconceptions of the Earth-Moon-Sun system emerged as a result of (1) cognitive difficulty in coordinating visual information from different perspectives; (2) misinterpreting salient features of the VSS visual representation; (3) ignoring the 3D nature of the Moon's relative motion, together with incorrect perception of the Moon's and the Earth's relative size and distance; and (4) the inability to mentally shift away from the Earth's frame of reference. These findings have significant bearing on our understanding of the educational potential and possible pitfalls of learning via virtual reality environments. The learning should be accompanied by suitable scaffolding and guided reflection to minimize the emergence of alternative astronomical conceptions. Designing additional navigation tools would empower the learners' perceptual and cognitive system.