A common problem in many schools is the lack of equipment and materials in their science laboratories due to both limited budget available to the school and high maintenance cost of the lab. The latest technological advancements provide great opportunities for schools to go over the budget and cost issues by using 3D virtual learning environments that support simulations and observations of various experiments. A 3D immersive computer-based Physics educational application that teaches water cycle in nature and precipitation formation concepts through virtual reality and experimental virtual laboratory simulations was designed and developed as part of European Horizon 2020 NEWTON Project. The application was employed and evaluated as part of a case study carried out in a secondary school in Dublin, Ireland. Children of age 12-13 years old from two classes took part in the study and were divided in two groups: one control group with 25 children, and one experimental group with 27 children. This paper presents an analysis of the user experience and usability results of the developed application, showing a high user experience score. The experimental group students also found the application enjoyable and they would like to take part in such novel-approach lessons more often.