This paper presents an integrated educational methodology to provide better, more extensive training to students in engineering disciplines. The methodology integrates both existing and ad hoc tools to improve mainly the following skills: holistic and comprehensive views of real problems, working in teams, communication abilities, and handling advanced numerical models and scientific computing. Experience by the authors with the implementation of the proposed methodology revealed a significant increase in the motivation and participation of the students: the more aware of the learning process they are, the more confident and motivated they feel. The implemented tools also help trigger student awareness towards a multidisciplinary, integrated and sustainable approach to face engineering problems, facilitating receptiveness to working with nature strategies. This methodology was developed for the field of marine and coastal engineering to overcome upcoming challenges such as problems due to climate change. Nevertheless, it can be easily extended to other engineering disciplines also pertaining to environmental problems and sustainability.