We developed a 5 population stochastic metapopulation model with key processes and threats relevant to lungfish, including: variability in habitat quality/quantity (variable recruitment opportunities as a result of variable habitat); variable recruitment success in response to flow management; and fish passage including mortality associated with passage over/through barriers, spillway stranding, and loss to estuaries below the limit of freshwater extent, including flood events. We model the inclusion of fishways and alternately the removal of spillway stranding mortality, flood frequency in the face of climate change and a pre-development construct for comparison. Modelling shows a benefit to the metapopulation with the inclusion of a fishway, potentially reducing risk close to pre-development levels, and a detriment to the mid-Brisbane River population with frequent large floods. This approach with the latest ecological understanding of lungfish ecology incorporated allows managers to test potential management interventions on a long-lived species where the effects of interventions may not be understood for decades.