How, when and what kind of learning takes place are key questions in all educational environments. School graduates are expected to have reached a development level whereby they have, among many fundamental skills, the ability to think critically, to plan their studies and their future, and to integrate knowledge across disciplines. However, it is challenging to develop these skills in schools. Following existing curricula, disciplines are often taught separately and by different teachers, making it difficult for students to connect knowledge studied and learned from one discipline to that of another discipline. The Next Generation Science Standards on teaching and learning natural science in the United States point out important crosscutting concepts in science education (NGSS, 2013). In Estonia, similar trends are leading to an emphasis on the need to further develop scientific literacy skills and interdisciplinary learning in students. The changing environment around us must be reflected in changes in our school system. In this paper, we report on research that intends to answer the questions: (a) “How much do Estonian students develop an interdisciplinary understanding of science throughout their high school education?”, and (b) “Is their thinking more interdisciplinary after two years of studies in an Estonian high school?” Additionally, we analyzed the results based on the type of school the students attended, and we examined the use concept mapping to assess interdisciplinary learning. This research is part of an overall study that involved students from 44 Estonian high schools taking a science test similar to the three-dimensional Programme for International Student Assessment (PISA) test (hereafter called PISA-like multidimensional test) as well as constructing concept maps, while in 10th and 12th grade. In this paper, we report on the analysis of the results for 182 of the students, concentrating on the analysis of the concept maps they constructed. The results suggest that there were changes in the students’ interdisciplinary knowledge, but these were small and varied depending on the students’ school type. They also suggest that changes may be needed in the Estonian educational system to increase the students’ level of interdisciplinary understanding of science.