Using the three-phase cooperation model and analysing projects based on their cooperation demands in the planning, implementation and operation phases, this article answers three main questions for each of the above-mentioned phases: (i) How and between which systems do cross-connections occur? (ii) Which actors are involved in those phases? (iii) Who needs to participate in which type of governance to achieve a better, more structured process of cross-connection control? The article refers to the world's largest novel water system in the Chinese city of Qingdao where a Resource Recovery Centre (RRC) providing the treatment of greywater for domestic and landscape reuse for 12,000 inhabitants has been implemented. A systematic interdisciplinary analysis of cross-connections leads to the conclusion that the approach to source separation needs to be complemented by governance instruments. These governance instruments derived from the actors identified by the cooperation management approach comprise processes of deliberation and communication, qualification and certification, final approval and inspection, as well as learning and evaluation.