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It was known that utilizing online discussion forum had an effect in increasing the understanding of the students of the class. To analyze the online learning experience, the Community of Inquiry (CoI) model is proposed. The CoI model divides the dynamics online learning process as social presence, teaching presence, and cognitive presence. This study aims to compare the application of CoI in Soil Mechanics course under the Civil Engineering Department at a large public university in Indonesia. The students of Soil Mechanics course were given a problem-based online discussion with two different types of discussion for two materials. The first one was a case study of Consolidation Settlement in a Collaborative Learning while the second one was a case study of Seepage case in a Free Discussion. Through quantitative analysis of the students- discussion transcript, it was found that cognitive and teaching presence were higher than social presence. Finally, through interview to students, it was found that students with active participation had better understanding and grades compared to passive students.