In this overview (introductory article to a special issue including 14 papers), we consider all main types of natural and artificial inland freshwater habitas (fwh). For each type, we identify the main biodiversity patterns and ecological features, human impacts on the system and environmental issues, and discuss ways to use this information to improve stewardship. Examples of selected key biodiversity/ecological features (habitat type): narrow endemics, sensitive (groundwater and GDEs); crenobionts, LIHRes (springs); unidirectional flow, nutrient spiraling (streams); naturally turbid, floodplains, large-bodied species (large rivers); depth-variation in benthic communities (lakes); endemism and diversity (ancient lakes); threatened, sensitive species (oxbow lakes, SWE); diverse, reduced littoral (reservoirs); cold-adapted species (Boreal and Arctic fwh); endemism, depauperate (Antarctic fwh); flood pulse, intermittent wetlands, biggest river basins (tropical fwh); variable hydrologic regime—periods of drying, flash floods (arid-climate fwh). Selected impacts: eutrophication and other pollution, hydrologic modifications, overexploitation, habitat destruction, invasive species, salinization. Climate change is a threat multiplier, and it is important to quantify resistance, resilience, and recovery to assess the strategic role of the different types of freshwater ecosystems and their value for biodiversity conservation. Effective conservation solutions are dependent on an understanding of connectivity between different freshwater ecosystems (including related terrestrial, coastal and marine systems).

Lepidocharontidae Galassi & Bruce, fam. n. is erected, containing Lepidocharon Galassi & Bruce, gen. n. and two genera transferred from the family Microparasellidae Karaman, 1934: Microcharon Karaman, 1934 and Janinella Albuquerque, Boulanouar & Coineau, 2014. The genus Angeliera Chappuis & Delamare Deboutteville, 1952 is placed as genus incertae sedis in this family. The Lepidocharontidae is characterised by having rectangular or trapezoidal somites in dorsal view, a single free pleonite, a tendency to reduction of the coxal plates, and the unique uropodal morphology of a large and long uropodal protopod on which the slender uropodal exopod articulates separately and anteriorly to the endopod. Lepidocharon Galassi & Bruce, gen. n. has a 6-segmented antennula, a well-developed antennal scale (rudimentary exopod), long and slender pereiopods 1–7 directed outwards, coxal plates rudimentary, incorporated to the lateral side of the sternites, not discernible in dorsal view, the single pleonite narrower than pereionite 7, scale-like elements bordering the proximal part of male pleopod 1 on posterior side, and stylet-guiding grooves of male pleopod 1 which run parallel to the outer lateral margins of the same pleopod. Lepidocharon priapus Galassi & Bruce, sp. n., type species for the genus, and Lepidocharon lizardensis Galassi & Bruce, sp. n. are described from Lizard Island, northern Great Barrier Reef. The most similar genus is Microcharon, both genera sharing the same general organization of the male pleopods 1 and 2, topology and architecture of the stylet-guiding groove of male pleopod 1, morphology of female operculum, presence of 2 robust claws of different lengths on pereiopodal dactylus 1–7, not sexually dimorphic. Lepidocharon gen. n. differs from Microcharon in the shape of the pereionites, very reduced coxal plates, the presence of imbricate scale-like elements bordering the proximal postero-lateral margins of the male pleopod 1, and the topology of the pereiopods, which are ventro-laterally inserted and directed outwards in Lepidocharon gen. n. and dorso-laterally inserted and directed ventrally in Microcharon. Lepidocharon shares with the genus Janinella the morphology of the tergites and the reduced lacinia mobilis of the left mandible, but differs significantly from Janinella in having a well-developed antennal scale, very reduced coxal plates also in females bearing oostegites, the general morphology and spatial arrangement of the stylet-guiding groove of male pleopod 1 and the possession of a 6-segmented antennula. The family Microparasellidae is redefined as monotypic, the only genus being Microparasellus Karaman, 1933.

Biodiversity hotspots are routinely identified by grid‐based analyses, despite grids encompassing different habitats, thus hindering the potential to assess which habitat type accounts for the conservation priority assigned to a grid. In this study, we aimed at identifying the main hotspots for the conservation of the European stygobitic Crustacea Copepoda Harpacticoida at the groundwater habitat scale. A multi‐metric approach was used, based on six biodiversity indicators: species richness, endemicity, evolutionary origin, phylogenetic rarity, taxonomic distinctness, habitat specificity. The Hot Spot Analysis, based on the statistics Getis‐Ord Gi*, was used to compare the local to the global average values of each indicator to identify hotspots of conservation. The operational units used to perform the analyses were the groundwater habitat types, in order to gather all the possible patterns of spatial occupancy in terms of habitat variability. Eight biodiversity hotspots of stygobitic Crustacea Harpacticoida were highlighted: 1) the Pyrenees (Spain and France), 2) the Jura Massif (France), 3) the Alpine arc (France, Switzerland and Italy) embracing southward the River Po alluvial plain and the Slovenian External Dinarides, 4) the Central Apennines (Italy), 5) the Carpathian and Balkan mountains in Romania and at the boundary between western Bulgaria and north‐west Macedonia, 6) the Dinaric Alps (from Croatia to Albania), 7) the Sardinia Island, 8) an area in central‐northern Europe embracing Denmark, the Netherlands and Germany. The hotspots showed a clear spatial distribution in southern Europe where they were distributed predominantly south to the 45th parallel, in line to what reiteratively observed in previous studies. Many hotspots embraced more than one habitat type. The adoption of discrete groundwater habitat types as working spatial units rather than grids provided a higher resolution of where the stygobitic harpacticoid species effectively live, with the possibility of intervening more precisely to preserve them and their habitats.

The distribution patterns of stygobitic crustacean harpacticoids at the boundaries of three different groundwater habitat types in Europe were analysed through a GIS proximity analysis and fitted to exponential models. The results showed that the highest frequency of occurrences was recorded in aquifers in consolidated rocks, followed by the aquifers in unconsolidated sediments and, finally, by the practically non-aquiferous rocks. The majority of the stygobitic harpacticoid species were not able to disperse across the boundaries between two adjacent habitats, with 66% of the species occurring in a single habitat type. The species were not evenly distributed, and 35–69% of them occurred from 2 to 6 km to the boundaries, depending on the adjacent habitat types. The distribution patterns were shaped by features extrinsic to the species, such as the hydrogeological properties of the aquifers, and by species’ intrinsic characteristics such as the preference for a given habitat type and dispersal abilities. Most boundaries between adjacent habitat types resulted to be “breaches”, that is transmissive borders for stygobitic harpacticoids, while others were “impermeable walls”, that is absorptive borders. Our results suggest that conservation measures of groundwater harpacticoids should consider how species are distributed within the different groundwater habitat types and at their boundaries to ensure the preservation of species metapopulations within habitat patches and beyond them.

We introduce a suite of software tools aimed at investigating multiple bio-ecological facets of aquatic Groundwater Dependent Ecosystems (GDEs). The suite focuses on: (1) threats posed by pollutants to GDE invertebrates (Ecological Risk, ER); (2) threats posed by hydrological and hydromorphological alterations on the subsurface zone of lotic systems and groundwater-fed springs (Hydrological-Hydromorphological Risk, HHR); and (3) the conservation priority of GDE communities (Groundwater Biodiversity Concern index, GBC). The ER is assessed by comparing tolerance limits of invertebrate species to specific pollutants with the maximum observed concentration of the same pollutants at the target site(s). Comparison is based on an original, comprehensive dataset including the most updated information on tolerance to 116 pollutants for 474 freshwater invertebrate species. The HHR is assessed by accounting for the main direct and indirect effects on both the hyporheic zone of lotic systems and groundwater-fed springs, and by scoring each impact according to the potential effect on subsurface invertebrates. Finally, the GBC index is computed on the basis of the taxonomical composition of a target community, and allows the evaluation of its conservation priority in comparison to others.

Groundwater invertebrate communities in karst landscapes are known to vary in response to multiple environmental factors. This study aims to explore the invertebrate assemblages’ composition of an Apennine karst system in Italy mainly described by the Rio Gamberale surface stream and the Stiffe Cave. The stream sinks into the carbonate rock and predominantly feeds the saturated karst into the cave. For a minor portion, groundwater flows from the epikarst and the perched aquifer within it. The spatial distribution of the species belonging to the selected target group of the Crustacea Copepoda between the surface stream and the groundwater habitats inside the cave highlighted a different response of surface-water species and obligate groundwater dwellers to the hydrogeological traits of the karst unit. Our results suggest that fast endorheic infiltration routes promoted the drift of epigean species from the surface to groundwater via the sinking stream while most of the obligate groundwater dwellers come from the perched aquifer in the epikarst from diffuse infiltration pathways.