Managing freshwater resources sustainably under future climatic and hydrological uncertainty poses novel challenges. Rehabilitation of ageing infrastructure and construction of new dams are widely viewed as solutions to diminish climate risk, but attaining the broad goal of freshwater sustainability will require expansion of the prevailing water resources management paradigm beyond narrow economic criteria to include socially valued ecosystem functions and services. We introduce a new decision framework, eco-engineering decision scaling (EEDS), that explicitly and quantitatively explores trade-offs in stakeholder-defined engineering and ecological performance metrics across a range of possible management actions under unknown future hydrological and climate states. We illustrate its potential application through a hypothetical case study of the Iowa River, USA. EEDS holds promise as a powerful framework for operationalizing freshwater sustainability under future hydrological uncertainty by fostering collaboration across historically conflicting perspectives of water resource engineering and river conservation ecology to design and operate water infrastructure for social and environmental benefits.