Understanding chemistry includes the ability to think on three levels: the macroscopic level, the symbolic level, and the level of particles--sub-microscopic level. Pupils have the most difficulty when trying to understand the sub-microscopic level because it is outside their range of experience. A virtual laboratory enables a simultaneous demonstration of all three levels of a chemical concept along with dynamic visualisation at the submicroscopic level. This study presents the effective usage of a virtual laboratory that can overcome the gap between the previously-mentioned conceptual levels. We carried out a didactic experiment to test the effectiveness of a virtual laboratory that enables dynamic visualisation. The experiment involved seventh-grade pupils (N = 109) from five different primary schools in Slovenia. We asked ourselves the question as to whether the learning outcomes of pupils are better when they use a virtual laboratory rather than in science classes without a virtual laboratory where dynamic visualisation at the sub-microscopic and sub-micro levels are only explained by means of static demonstrations. A virtual laboratory has many significant advantages. The results of the didactic experiment showed that, in terms of knowledge acquisition, using a virtual laboratory is better than science classes without visualisation elements.