This paper discusses exclusively the dependency between the ecological and hydro-geochemical criteria used to classify hydrogeological formations and provides an overview of the most measurable environmental factors characterizing the groundwater ecosystem. Compact, porous, fractured and karstic formations are complex hydro-geomorphological units which store variable amounts of water. They are considered the main habitats for stygofauna in many regions worldwide. The hydrogeological situation of a groundwater system varies spatially (both laterally and vertically) and temporally at different scales. Moreover, different factors (e.g. surface and groundwater interaction (hydrological exchange), precipitation, land use, land cover) play an active role in classifying groundwater systems. Therefore, many concepts have already been proposed to classify these systems. This paper focuses on the relationships between communities of groundwater invertebrates (occurrence, distribution and diversity of stygofauna) and special hydrogeological indicators, by examining the hypotheses and results of previous literature.