In South Australia, discrete populations of bottlenose dolphins inhabit two large gulfs, where key threats and population estimates have been identified. Climate change, habitat disturbance (shipping and noise pollution), fishery interactions and epizootic events have been identified as the key threats facing these populations. The Population Consequences of Disturbance (PCoD) framework has been developed to understand how disturbances can influence population dynamics. We used population estimates combined with population specific bioenergetics models to undertake a partial PCoD assessment, comparing how the two populations respond to the identified regional threats. Populations were modeled over a 5 year period looking at the influence of each disturbance separately. As expected, the most extreme epizootic and climate change disturbance scenarios with high frequency and intensity had the biggest influence on population trends. However, the magnitude of the effect differed by population, with Spencer Gulf showing a 43% and Gulf St Vincent a 23% decline under high frequency and high impact epizootic scenarios. Epizootic events were seen to have the strongest influence on population trends and reproductive parameters for both populations, followed by climate change. PCoD modeling provides insights into how disturbances may affect different populations and informs management on how to mitigate potential effects while there is still time to act.