The Chalk aquifer is often considered as a single, homogeneous, isotropic groundwater system in regional groundwater management studies, even though it has been subdivided into several different lithostratigraphic units. Low-permeability layers, including marl bands and hardgrounds, extend on a regional scale and define different layers within the Chalk. Four case studies in different locations of the Chalk aquifer of SE England are presented: (1) a multi-level observation borehole in the Upper Colne catchment in Hertfordshire; (2) different water levels in shallow and deep boreholes in the River Ver catchment; (3) artesian conditions and rises in the groundwater level during drilling in the Chiltern Hills; and (4) groundwater level separation in a public water supply borehole in Kent. The evidence clearly shows a layered system in the Chalk and vertical hydraulic discontinuity within the studied sequences. The current conceptual model of the Chalk aquifer should be enhanced to include this new understanding and to update the existing numerical groundwater models. This will, in turn, increase confidence in the current decision support tools for environmental sustainability and the management of water resources in the Chalk aquifer.