For many freshwater fish there is often little known about the spatio-temporal drivers of their distribution, particularly among different life stages, making their conservation challenging. We used two-stage hurdle models to investigate drivers of occurrence and abundance for locally threatened adult and juvenile northern river blackfish in the upper Condamine River, Queensland, Australia. Our results demonstrate that there are different processes driving occurrence versus abundance between the two life-history stages. Both adult and juvenile occurrence were negatively associated with high magnitude, extended warming events, suggesting blackfish are thermally restricted to cooler headwaters. Furthermore, juvenile fish demonstrated increased sensitivity to high stream temperatures as compared to adults. In contrast, drivers of abundance differed between life-history stages. Adult fish were negatively associated with increased fine sediment loads, while juveniles were negatively associated with a hydrologically-active inverse-distance-weighted grazing metric that accounted for the greater influence of grazed land close to stream or in areas of high overland flow. By teasing out environmental drivers affecting multiple life-history stages of a locally threatened headwater species, our approach allows us to provide direct management recommendations for best conserving this species, as well as ecologically similar headwater fishes and their associated habitats.