Laboratory work in science education is essential for students’ conceptual understanding of natural phenomena. Computer-simulated laboratory experiments have been proposed to facilitate traditional laboratory work. A virtual laboratory was designed to enable students to collaboratively discover the concept of gas solubility in water at different physiological conditions. The virtual laboratory was developed through a design experiment involving three successive versions with different guiding structures. Analysis of 12 dyads’ reasoning about gas solubility in water revealed that the problem was not primarily for the students to realise how the volume of gas changed, but rather to understand the concept of solubility of gases. It was also observed how the guiding structures within the three different versions influenced the students’ reasoning about the concept. The analysis indicates that the affordances of virtual laboratories might, to a certain extent, enhance joint discovery of a scientific concept.