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The fauna in the hyporheic zones of rivers has been relatively well studied but that from the phreatic zone remains comparatively unknown and there are few investigations into deeper intergranular aquifers (over 30 m in depth) due to technical difficulties. Two shallow boreholes of 29 m depth and two deep boreholes of 100 m depth, both near Ljubljana (Slovenia), were sampled more than 30 times between 14 January 2008 and 3 March 2009. On each occasion 14.4 to 18.0 m3 of water were abstracted using a high-capacity pump, then filtered by means of a plankton net with a mesh size of 60 µm. Organisms larger than 2 mm were damaged by the pump rotors, but their identification was still possible, while smaller representatives of the Copepoda (Crustacea) passed the rotors without damage. A near-by artesian borehole was sampled on 6 occasions. Water chemistry, physical properties and faunal composition analyses were carried out for each borehole. A total of 32 taxa, 24 of which were stygobites, were identified. Copepoda alone were represented by 16 species, 15 of which were stygobites. The shallow boreholes differ from the deep boreholes in their higher temperatures and higher concentrations of K+, Na+, Ca2+, Mg2+ and SO42- ions. The copepod communities in samples from the shallow boreholes differ sharply from those from the deep boreholes. There were also clear differences between shallow boreholes in two aquifers located a few kilometres apart, in physical and chemical characteristics as well as in fauna composition. Taxa with different ecological affinities, collected from groundwater, are indicators of hydraulic connections between different parts of an aquifer as well as of communication between surface and subsurface water bodies. The present study suggests that subterranean fauna, as well as epigean fauna, can provide effective support for classical dye/salt tracing experiments.