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Urban transformations involve complex problems; they require a sound theoretical framework able to grasp their full complexity, and a methodological approach allowing for using the full potential of both practice and science. The Human–Environment System (HES) framework offers the former, the transdisciplinary (td) case-study design the latter. We introduce both by referring to a case study with more than 200 participants on leisure traffic in the city of Basel. The project was organized as a “strong” transdisciplinary process, ie, with joint leadership and institutionalized collaboration of practice and science at all project levels. From a coupled HES perspective, we analyzed different social groups in four contrasting city districts. Different scenarios of future development for both lifestyles and the districts were constructed and assessed from a sustainability perspective. Further, detailed preference information was elicited from 120 persons. Car-centered lifestyles are clearly less preferred than car-free lifestyles. Upgrading city districts assessed differently between the districts. We discuss the potential and challenges of HES-based td processes for guiding and facilitating sustainable urban transformations.