Increasing demand for water and a desire for greater human water security has facilitated the global expansion of dams, with river regulation acknowledged as the leading cause of biodiversity decline in rivers. Native biota within these stressed systems are also impacted by reductions in habitat availability, decreased hydraulic diversity, increased sedimentation, movement barriers, invasive species and altered flows that may profoundly change the character and functioning of rivers. Construction or enlargement of reservoirs is continuing, and whilst downstream impacts are often considered, upstream impacts receive far less attention. We develop a population model to examine the impacts of reservoir expansion on a threatened riverine species in South Eastern Australia: the two-spined blackfish. We examined two processes, loss of breeding habitat and increased predation, directly linked to reservoir expansion as well as a broader threat of recruitment failure due to sedimentation. These threatening processes were assessed using the expected minimum population size as an indicator of risk. As is often the case for threatened species, limited data were used to parameterise the model and sensitivity analysis performed to assess the appropriateness of the model parameterisation. The outcomes indicate that the two-spined blackfish population is vulnerable to the loss of breeding habitat particularly if two-spined blackfish are unable to spawn in the larger dam, although this vulnerability is ameliorated if the whole river is accounted for. Including possible impacts from the resident trout population for the whole river, indicates the two-spined blackfish to be vulnerable to low level predation particularly if the trout population have a high growth rate. Population modelling has rarely been used to predict the consequences of dam construction on aquatic species/communities. The example here shows it to be a powerful tool to visualise and quantify potential biodiversity outcomes.