Groundwater is an important resource, not least in south-eastern areas of England, where chalk is the dominant aquifer. Such chalk-fed stream ecosystems are rich and highly productive, they have particularly important springhead wetlands, and are characterised by fast-growing trout populations. The legislative framework, founded on the Minimum Acceptable Flow concept, is in place to protect these stream ecosystems. In surface water dominated catchments, normal operational rules use prescribed (usually hands-off) flows to protect in-river needs. Such rules are inappropriate for most groundwater-dominated catchments because of the slow response between change in groundwater abstraction and river flow. This paper illustrates the use of an Ecologically Acceptable Flow Regime (i) to determine a MAF based on the annual volume of flow, described as a flow duration curve, to protect the riverine ecosystem at the catchment scale, and (ii) to set a prescribed flow that must be maintained locally by river support.