AbstractViruses and bacteria which are characterized by finite lives in the subsurface are rapidly transported via fractures and cavities in fractured and karst aquifers. Here, we demonstrate how the coupling of a robust outcrop characterization and hydrogeophysical borehole testing is essential for prediction of contaminant velocities and hence wellhead protection areas. To show this, we use the dolostones of the Permian Magnesian Limestone aquifer in NE England, where we incorporated such information in a groundwater flow and particle tracking model. Within this aquifer, flow in relatively narrow (mechanical aperture of ~ 10⁻¹–1 mm) fractures is coupled with that in pipe cavities (~ 0.20-m diameter) following normal faults. Karstic cavities and narrow fractures are hydraulically very different. Thus, the solutional features are represented within the model by a pipe network (which accounts for turbulence) embedded within an equivalent porous medium representing Darcian flowing fractures. Incorporation of fault conduits in a groundwater model shows that they strongly influence particle tracking results. Despite this, away from faulted areas, the effective flow porosity of the equivalent porous medium remains a crucial parameter. Here, we recommend as most appropriate a relatively low value of effective porosity (of 2.8 × 10⁻⁴) based on borehole hydrogeophysical testing. This contrasts with earlier studies using particle tracking analyses on analogous carbonate aquifers, which used much higher values of effective porosity, typically ~ 10² times higher than our value, resulting in highly non-conservative estimates of aquifer vulnerability. Low values of effective flow porosities yield modelled flow velocities ranging from ~ 100 up to ~ 500 m/day in un-faulted areas. However, the high fracturing density and presence of karstic cavities yield modelled flow velocities up to ~ 9000 m/day in fault zones. The combination of such flow velocities along particle traces results in 400-day particle traces up to 8-km length, implying the need for large well protection areas and high aquifer vulnerability to slowly degrading contaminants.