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The article presents challenges associated with understanding complex systems in science education. Complex systems possess hierarchical nature with various interacting levels. The aggregate nature of the complex system is unpredictable from isolated components and occurs by the interaction of multiple components. As the learning of complex systems involves several difficulties, these systems are basis of many areas of learning, having the ability to integrate across various learning disciplines. There is an integration of biology, chemistry, physical science and social science while learning aquatic systems. According to researchers, the ability of students to learn about complex systems as well as other challenging topics depends to a greater extent on the disposal of such processes to plan, sustain and reflect on the complex mechanisms underlying learning about complex systems. Complex systems can also be studied well with the help of computers. Computer-assisted learning environments can help students to learn complex systems efficiently.