The catchment of the iconic Finke River is celebrated for its biodiversity. Situated within the endorheic Lake Eyre Basin (LEB), the area is both arid and hydrologically isolated from other major LEB rivers. In the context of the arid zone the fish assemblage of the Finke catchment is diverse (9 species, including 3 endemics), yet until recently little was known about fish species’ distribution, habit preferences or the distribution of drought refuges. Monitoring for the Lake Eyre Basin Rivers Assessment (LEBRA) commenced in 2011 and is the first systematic population sampling in this catchment. LEBRA has been the catalyst for sampling at many additional sites and the collective data set provides a baseline for both future condition assessment and the necessary underlying ecological understanding. Analysis shows clear patterns in distribution and habitat preference of species, with salinity being a key driver. Differences in the salt tolerance between species not only influence distribution but also the function of particular waterholes as drought refuges. Due to complex sub-surface saline groundwater inputs, some waterholes rapidly increase in salinity after rain-fed flow events, including some of the permanent refuge pools. Some non-permanent but long-lasting pools reach very high salinities at which only the most tolerant species persist. In contrast, some waterholes persist as fresh or semi-saline habitats, even in droughts, despite evaporative concentration. Whilst salinity is an unambiguous driver in this system, other habitat parameters must also be considered to better understand population dynamics, distribution and assemblage at scales from waterhole to catchment.