Present and future social and ecological challenges are complex both to understand and to attempt to solve. To comprehend the complex systems underlying these issues, students need systems thinking skills. However, in science education, a uniform delineation of systems thinking across contexts has yet to be established. While there seems to be consensus on a number of key skills from a theoretical perspective, it remains uncertain whether it is possible to distinguish levels of systems thinking, and if so, how they would be determined. In this study, we investigated the impact of the specifics of a system on the skills and levels of systems thinking. We administered a 36‐item multiple‐choice test to 196 Grade 5 and 6 students. For our analysis, we followed a quantitative approach, applying a systems thinking model that incorporates the latest insights on the levels and skills of systems thinking in geography to the context of ecology. By following an Item Response Theory approach, we confirmed a set of systems thinking skills that are necessary to understand complex systems in ecology: identifying system organization, analyzing system behavior, and system modeling. We examined whether individual skill levels can be distinguished to determine whether a system's general principle or system‐specific features cause difficulty for students. Our results indicate that system specifics, such as type of relation within ecosystems (e.g., predator–prey), appear to determine the formation of levels. Students struggled most with the difference between basic, direct cause‐and‐effect relationships and indirect effects. Once they understood the relevance of indirect relationships in moderately complex systems, a further increase in complexity caused little additional difficulty. Accordingly, we suggest that systems thinking should be examined from a variety of perspectives. To promote interdisciplinary learning, a systems thinking model that defines key commonalities across fields while leaving space for system specifics is needed.