(1) The distribution of organisms that inhabit patchy systems is dictated by their ability to move between patches, and the suitability of environmental conditions at patches to which they disperse. Understanding whether the species involved are identical to one another in their environmental requirements and their responses to variance in their environment is essential to understanding ecological processes in these systems, and to the management of species whose patchy and limited distributions present conservation risks. (2) Artesian springs in Australia’s arid interior are “islands” of hospitable wetland in uninhabitable “oceans” of dry land and are home to diverse and threatened assemblages of endemic species with severely restricted distributions. Many have strict environmental requirements, but the role of environmental heterogeneity amongst springs has rarely been considered alongside conventional patch characteristics (isolation and patch geometry). (3) We quantified environmental heterogeneity across springs, and the relationship between spring size, isolation (distances to neighbours) and environmental quality (depth, water chemistry), and patterns of occupancy and population persistence of six endemic spring snail species, all from different families, and with all restricted to a single <8000 ha system of springs in Australia. To do so, a survey was conducted for comparison against survey results of almost a decade before, and environmental variables of the springs were measured. Many of the snail species occupied few sites, and environmental variables strongly covaried, so an ordination-based approach was adopted to assess the relationship between environmental measures and the distribution of each species, and also whether springs that held a higher diversity of snails had specific characteristics. (4) Each snail species occupied a subset of springs (between 5% and 36% of the 85 sampled) and was associated with a particular set of conditions. Of the six species considered in further detail, most were restricted to the few springs that were large and deep. Species in family Tateidae were distinct in having colonised highly isolated springs (with >300 m to nearest neighbour). Springs with highest diversity were significantly larger, deeper and had more numerous neighbours within 300 m than those devoid of endemic snails, or those with low diversity. (5) Although spring size and isolation affect patterns of occupancy, the six snail species had significantly different environmental requirements from one another and these correlated with the distribution pattern of each. Approaches that ignore the role of environmental quality—and particularly depth in springs—are overlooking important processes outside of patch geometry that influence diversity. These organisms are highly susceptible to extinction, as most occupy less than 3 ha of habitat spread across few springs, and habitat degradation continues to compromise what little wetland area is needed for their persistence.