A teaching‐learning methodology by using computational software in teaching groundwater pumping in aquifer system is presented. In order to ensure the students grasp the theory and method of groundwater flow, as well as land subsidence due to pumping groundwater. The computational software‐COMSOL is used to solve the fully coupling equilibrium equations and flow equation. The assessment of the instructor includes: homework, group discussions, and small projects, which help to figure out the degree of understanding of students’ knowledge points. In addition, the teachers prompt students to reflect on what they have learned and use the obtained responses to evaluate the effectiveness of the course. The survey finds that most students believe that they can understand the equilibrium equations and the fully coupled flow equation according to the teacher's instructs, and can perform computer operations independently. The final test results show that this teaching‐learning methodology by using computational software has a very good teaching effect.