Factories consist of production equipment, technical building services (TBS) and building shell, which are connected through interdependent energy and resource flows. The relationship of water and energy flows (water–energy nexus) is an important example—it couples energy and water demands in manufacturing (e.g. cooling, heating, cleaning) with TBS such as boilers, cooling systems or water treatment. While being intensively discussed in context of e.g. industrial ecology, there is no systematic methodological support to improve the water–energy nexus towards sustainability in manufacturing. Therefore, the paper provides a framework and methodology for systematic improvement, which is applied within a case study.