Groundwater use can reduce streamflow by reducing groundwater flows into streams and/or increasing losses from the stream into the aquifer (‘streamflow depletion’). Streamflow depletion can impact aquatic ecosystems through changes in the availability and temperature of surface water. Regions with a combination of groundwater withdrawals and groundwater-dependent resources therefore require management strategies that respond to the needs of both humans and aquatic ecosystems. Here, we review and evaluate opportunities and challenges for applying an environmental flows approach to streamflow depletion management based on functional flows and the Ecological Limits of Hydrological Alteration (ELOHA) frameworks. We highlight the need for explicit recognition of temperature in streamflow depletion science, especially given the realities of climate change. Using a demonstrative analysis on Wisconsin streams, we show that both the magnitude and variability of streamflow and stream temperatures are likely to be impacted by groundwater withdrawal, with particular impacts on low flows during the baseflow period. Then, we evaluate potential challenges to integrating existing groundwater withdrawal management and environmental flows approaches and provide a pathway to address inherent tensions between these two frameworks. In particular, we find that uncertainty associated with the first two ELOHA steps (setting a baseline and classifying streams) can lead to substantially different estimates of ecological impacts in streamflow depletion contexts. Navigating these tensions requires stakeholder engagement throughout the process of setting acceptable management thresholds to move towards practical, management-focused integration of environmental flows and streamflow depletion science.