The well-known eco-efficiency concept helps to assess the economic value and resource burdens of potential improvements by comparison with the baseline situation. But eco-efficiency assessments have generally focused on a specific site, while neglecting wider effects, for example, through interactions between water users and wastewater treatment (WWT) providers. To address the methodological gap, the EcoWater project has developed a method and online tools for meso-level analysis of the entire water-service value chain. This study investigated improvement options in two large manufacturing companies which have significant potential for eco-efficiency gains. They have been considering investment in extra processes which can lower resource burdens from inputs and wastewater, as well as internalising WWT processes. In developing its methodology, the EcoWater project obtained the necessary information from many agents, involved them in the meso-level assessment and facilitated their discussion on alternative options. Prior discussions with stakeholders stimulated their attendance at a workshop to discuss a comparative eco-efficiency assessment for whole-system improvement. Stakeholders expressed interest in jointly extending the EcoWater method to more options and in discussing investment strategies. In such ways, optimal solutions will depend on stakeholders overcoming fragmentation by sharing responsibility and knowledge.