A qualitative model of a system is an abstraction that captures ordinal knowledge and predicts the set of qualitatively possible behaviours of the system, given a qualitative description of its structure and initial state. This paper examines an innovative approach to science education using an interactive learning environment that supports learners in expressing and simulating conceptual knowledge by building qualitative models in ecology. The learning environment and tools are being developed as part of the DynaLearn qualitative modeling research project, funded by the European Union's 7th framework programme and carried out by a consortium of eight participant universities. In summing up the results, it is clear that from the perspective of systems thinking, the modeling activity affected students' perception of systems making them able to represent it in a more dynamic and comprehensive way.