Rainfall is a key process in the water cycle, the most structured scientific knowledge about water movement on Earth. Nevertheless, despite being a common topic covered in school science, it entails several cognitive difficulties for young children. This study uses a pictorial task and semi-opened questions to examine primary (11/12 years old) and secondary (12/13 years old) students' understanding of the elements and processes involved in the hydrologic cycle and how they are integrated into their explanations regarding the rainfall phenomenon. Overall, we have found that the studied children's (n = 246) conceptual knowledge increases with age. However, they have an incomplete perception of the mechanism of rainfall and its integration into the water cycle. In fact, not all the students have a cyclic notion of water dynamics; they also miss the inclusion and role of groundwater in water systems and present misconceptions regarding key processes, such as condensation and evaporation. Regarding the two diagnostic tools (drawings and questionnaires) used to study children's understanding, although questionnaires seem more appropriate for assessing lower conceptual levels, each methodological approach is useful for detecting different key concepts and misconceptions related to the rainfall phenomenon and related water cycle. Consequently, a mixed research design using different methods is advised for a comprehensive study of students' conceptions.