A new multi-scale groundwater modelling methodology is presented to simulate pumped water levels in abstraction boreholes accurately within regional groundwater models. This provides a robust tool for assessing the sustainable yield of supply boreholes, thus improving our understanding of groundwater availability during drought. Under UK legislation water companies are required to quantify the reliable, or deployable, output (DO) of all groundwater and surface water sources under drought conditions. However, there is a current lack of appropriate tools for assessing groundwater DO, especially for hydrogeologically complex sources. This is a particular issue for sources in the Chalk aquifer, which is vertically heterogeneous and closely linked with the surface water system. The DO of an abstraction borehole is influenced by processes operating at different scales. The multi-scale model incorporates these processes, providing a new and unique method for simultaneously representing regional groundwater processes, local-scale processes, and features of a borehole. The 3D borehole-scale model solves the Darcy-Forchheimer equation in cylindrical co-ordinates to simulate both linear and non-linear radial flow to a borehole. It represents important features of the borehole itself and incorporates horizontal and vertical aquifer heterogeneity. The radial flow model is embedded within a Cartesian grid using a hybrid radial-Cartesian finite difference method which has not previously been applied in the field of groundwater modelling. A novel methodology is developed to couple this model to a regional groundwater model, ZOOMQ3D, using the OpenMI model linkage software. This provides a flexible and efficient tool for assessing the behaviour of a groundwater source within its regional hydrogeological context during historic droughts and under climate change. The advantages of the new method for calculating the sustainable yield of abstraction boreholes are demonstrated through application to a Chalk supply borehole in the Thames Basin. The multi-scale methodology has many potential applications beyond DO, but provides a valuable tool for water companies to produce a more reliable and robust assessment of groundwater availability, in line with the current water resources planning guidelines.