Groundwater ecosystems comprising micro-organisms and metazoans provide an important contribution to global biodiversity. Their complexity depends on geology, which determines the physical habitat available, and the chemical conditions within it. Despite this, methods of classifying groundwater habitats using geological data are not well established, and researchers have called for higher resolution habitat frameworks. A novel habitat typology for England and Wales (UK) is proposed, which distinguishes 11 geological habitats (geohabitats) on hydrogeological principles and maps their distribution. Hydrogeological and hydrochemical data are used to determine the characteristics of each geo-habitat, and demonstrate their differences. Using these abiotic parameters, a new method to determine abiotic habitat quality is then developed. The geo-habitats had significantly different characteristics validating the classification system. Karstic and porous habitats were generally of higher quality than fractured habitats. All geo-habitats were highly heterogeneous, containing both high quality habitat patches that are likely to be suitable for fauna, and areas of low quality that may limit faunal distributions. Overall, 70 % of England and Wales are covered by lower quality fractured habitats, with only 13 % covered by higher quality habitats. The main areas of high quality habitats occur in central England as northsouth trending belts, possibly facilitating dispersal along this axis. They are separated by low quality geo-habitats that may prevent east-west dispersal of fauna. In south-west England and in Wales suitable geo-habitats occur as small isolated patches. Overall, this paper provides a new national-scale typology that is adaptable for studies in other geographic areas. Weitowitz et al., 2017. Hydrogeology Journal