The technological innovation systems (TIS) framework is one of the dominant perspectives in transitions studies to analyze success conditions and system failures of newly emerging technologies and industries. So far, TIS studies mostly adopted a rather harmonious view on the values of actors and by this were unable to address competition, conflicts and, in particular, battles over diverging directionalities within the system. To empirically assess this potential “harmony fallacy”, we identify values as part of underlying institutional logics of major organizations in the field of modular water technologies in Switzerland by means of 26 expert interviews. We show how logics may condition collaboration patterns and technological preferences. This analysis inspires key conceptual tasks of innovation system analysis, like the identification of system failures, the setting of appropriate system boundaries and the formulation of better policy recommendations.