The Australian lungfish, Neoceratodus forsteri, is one of the world’s oldest living vertebrate lineages, and is listed as a threatened species and requires immediate conservation management. Lungfish are a large-bodied species (1.5 m in length and 48 kg), in the wild may live up to 100 years maturing at around 10 years of age. We developed a stochastic population model that has been applied to each endemic population of lungfish in Australia and one introduced population, to provide insights into the appropriate management options and priorities for such a long-lived species as well as to help direct future research opportunities. The model has been developed as both a single population construct and as a metapopulation construct with up to three interacting populations to characterise the different river systems in which lungfish are found. For each location and each population, flow, spawning and movement rules were developed to capture the ecological and biological response of lungfish to its environment. The models use a common 80-year class matrix for this long-lived fish, informed by estimates of survival and fecundity rates, density-dependence, and habitat loss from variable river flows that impact eggs, larvae, and young-of-the-year fish. The models assess flow and flow-related effects on lungfish life-stages, where flows in spawning habitats drive population dynamics and determine rates of movement between populations. The model construct is most sensitive to survival estimates for juveniles, particularly 1- and 2-year-olds. Reproductive value is highest across ages 20 to 40 years, indicating that fish in these age classes make the greatest reproductive contribution to the population(s). Our modelling approach substantially advances conservation management of this iconic fish species as it integrates recent scientific knowledge and can be used to assess responses to management actions and recovery plans.