Increasing recognition of the importance of ecosystem services in water resources management has accelerated the development and application of environmental‐flows requirements for lotic ecosystems. However, most environmental‐flows management focuses on water infrastructure, such as dams or diversions, without explicitly taking groundwater into account and ignoring the importance of groundwater environmental flow contribution. In this study two methods for estimating groundwater environmental flow contributions are presented: (a) a groundwater‐centric method (based on the Sustainability Boundary Approach), which proposes that high levels of ecological protection are maintained if 90% of groundwater discharge is preserved, and (b) a surface water‐centric method (novel method), which quantifies groundwater environmental flow contributions from streamflow using region‐specific streamflow sensitivity metrics and local environmental‐flows policies. The two methods were tested in British Columbia, Canada, which has a diverse, complex, and highly coupled groundwater‐surface water system. The two methods gave comparable results in various hydro‐geoclimatic settings. Although British Columbia was used as a case study, this framework can be implemented across various spatial and temporal scales for different regions and globally, in data‐scarce, hydrologically complex landscapes. Application of these methods can aid in a robust and holistic assessment of environmental‐flows, taking into account the often‐missing groundwater component.