The Cam and Ely Ouse Chalk aquifer has been an important source of public water supply for over 100 years. In response to growing demand for water in the area in the 1970s and 1980 s, the National Rivers Authority developed the Lodes–Granta scheme to provide augmentation water to key rivers, subject to low flows. However, during the droughts in the late 1990s, the River Granta, which derives baseflow from the Chalk aquifer, was dry in some locations for several months. In response, the Environment Agency and Cambridge Water carried out investigations into the impacts of abstraction on the flow and ecology of the Granta and agreed to restrict abstraction from two operational groundwater sources during low flow periods. However, these abstraction restrictions could potentially result in a shortfall within the relevant public water supply zone under some climatic conditions and so Cambridge Water was considering increasing abstraction from an alternative source of groundwater within the catchment to retain the level of resilience of its supply. The Environment Agency was concerned that use of this abstraction could pose a risk of deterioration of the ecological status of the water body under the EU Water Framework Directive. This paper describes the investigations undertaken to assess the risk of deterioration and shows how these are being used to manage this risk going forward.