In this study we evaluate a project-based learning course called Applied Ecology, within the master program Sustainable Technology at the Division of Industrial Ecology, at KTH—Royal Institute of Technology in Stockholm, Sweden. The case study in the course is focused on the effects of a relatively large Bay, “Burgsviken”, situated on the island Gotland in the middle of the Baltic Sea, that has changed due to the eutrophication in the area. The eutrophication of the Bay has initiated bottom up processes of discussion and engagement among the stakeholders in the area, for the enhancement of the water quality and biological services of the bay, that would in turn improve fishing, swimming, biological diversity and tourism. There are several stakeholders involved in the project: a local non-profit organisation, farmers, entrepreneurs, authorities, permanent and seasonal inhabitants, researchers and others. The course is evaluated according to the methodology of Brundiers and Wiek (2013). Student evaluations have been conducted and analysed in relation to four phases: (1) Orienting phase, formulation of research question. (2) Framing phase, methodology and study planning. (3) Research phase, field study and other examinations. (4) Implementation phase, communication of the results with different stakeholders. The Applied Ecology course shares many of the positive features of other PPBL courses in the sustainability field—namely that it focuses on a real sustainability problem and that the student-centred learning approach and interactions between students and stakeholders make the student partnership in the project feel real, thus providing a practical insight of complex societal challenges. There are potential ways of improving all four phases of the course that were studied, but especially in the research phase and the implementation phase more efforts are needed. Feedback and reflections in the research phase could be improved by a clearer communication and to some extent changed pedagogical process through the course. All phases will be improved by increased communication before, during and after fieldwork between student, teachers and stakeholders.