Applying the environmental flows concept to human-altered lotic ecosystems continues to face many practical challenges and barriers. Here, we modify a previously proposed framework, the Eco-Engineering Decision Scaling, for application to part of the water supply system of Quito, Ecuador. Specifically, we used feedback from engineers and water managers to develop a common set of metrics for defining flow-ecology relationships and assess managed-flow impacts on stream ecology. At 12 sites over 3 years, we collected flow and benthic invertebrate data (taxonomic richness, taxa important for fish, functional feeding groups, and water quality-sensitive taxa) during wet and dry seasons. We then used these data to identify flow thresholds (relative to unmanaged flows) where flow withdrawal caused visible ecological impacts. For this system, reduction of flow to 20% of the annual median was detrimental to benthic communities, while reductions to 40% of the annual median flow caused a variety of responses in the system. A trade-off analysis of weighted metrics showed that a 50% benthic fauna richness could be sustained if dry season flows were maintained between 28% and 40% of the unmanaged median annual flow. This study provides a roadmap for bridging between eco-engineering theoretical frameworks and the adoption of the environmental flows concept as actionable management thresholds.