Streams are becoming increasingly fragmented by anthropogenic impacts related to altered thermal and hydrological regimes, dispersal barriers, land-use, introductions of non-native fish, habitat degradation, and altered disturbance regimes. Furthermore, relatively little is known about the ecology and spatio-temporal dynamics of a large proportion of freshwater fish populations and assemblages, making their conservation challenging. The general goal of my research was to improve ecological understanding of the drivers of fish distribution in upland streams, using the threatened Northern river blackfish (Gadopsis marmoratus - hereinafter blackfish) in the upper Condamine River and Spring Creek tributaries in Queensland, as a case study. While blackfish are still widespread throughout the Murray Darling Basin, anecdotal evidence suggests that historically, they were widely distributed throughout the entire upper catchment of the Condamine River, extending into the lowlands. In addition, results from contemporary research suggests that these fish may now be restricted to headwaters and tributaries. The aim of my research was to identify the variables that influence blackfish distribution in this upland system. More specifically, I tested the hypothesis that these fish are thermally restricted to their current habitat range. I asked whether there are different processes governing their occurrence versus abundance, and whether these vary between life-stages. In addition to examining static population structure I also examined the environmental determinants of juvenile recruitment in this system, and examined the spatial scales at which these take place.