Freshwater ecosystems are essential to peoples' economic, cultural, and social well‐being, yet are still among the most threatened ecosystems on the planet. Consequently, a plethora of recent regulations and policies seek to halt the loss of restore or safeguard freshwaters, their biodiversity, and the ecosystem services they provide. Ecosystem‐based management (EBM), an approach that considers human society as an integral part of ecosystems, is increasingly being promoted to help meet this challenge. EBM involves an overarching regulatory framework and local solutions with trade‐offs and compromises—factors that not only make decision processes complex but also provide the means for combining top–down regulation with bottom‐up priorities into collaborative management strategies. Although stakeholder participation is encouraged in most modern freshwater management, community values are often largely neglected. Here, we introduce a well‐known participatory decision support framework based on multicriteria decision analysis (MCDA) to operationalize EBM and promote community‐inclusive decision making in freshwater management. We explain the different steps that this approach comprises, which lead to the prioritization of a management strategy in a collaborative way. We also show how cultural values that inherently embed strong links between the environment and people can be used together with typical ecological and socio‐economic values. We illustrate the MCDA‐based EBM‐approach for New Zealand, one of the few countries in which regional freshwater management is mandated to uphold environmental quality standards, while safeguarding local community values and ecosystem services. Finally, we discuss some of the challenges, which are increasingly emerging as a result of mandated community collaboration in environmental management.