In this study, the VR 360° panoramic technology is used to develop a virtual wetland ecological system for applications in environmental education. The system provides a virtual wetland environment for autonomous exploration, where the user can conduct inquiry-based learning by cardboard VR to obtain essential information and concepts in ecological protection. It contains the learning contents of wetland ecology and creatures in Hsinchu coastal areas, northern Taiwan. To investigate the learning effectiveness of the VR system, we recruited 42 seventh graders as participants and divided them evenly into two groups. The experimental group used the virtual wetland ecological system for learning and the control group learned with conventional teaching materials. The differences of the experimental results indicated: (1) the experimental group showed a high degree of satisfaction after using the virtual wetland ecological system; (2) the learning achievement of the experimental group was significantly higher than that of the control group; (3) the learning motivation of the experimental group was significantly higher than that of the control group. The virtual wetland ecological system can enhance the learning effectiveness and learning motivation using low-cost cardboard glasses, so it is a suitable tool for promoting environmental education in remote areas.