In South Australia, discrete populations of bottlenose dolphins inhabit two large gulfs, Spencer Gulf and Gulf St Vincent. In each gulf, dolphin population abundance has been estimated and key threats; climate change, habitat disturbance (shipping and noise pollution), fishery interactions and epizootic events, identified. The Population Consequences of Disturbance (PCoD) framework was developed to understand how disturbances can influence population dynamics. We used population estimates combined with population specific bioenergetics models to undertake a PCoD assessment and compared how these two populations respond to the identified regional threats. Populations were modelled over a five year period looking at the influence of each disturbance separately. As expected, extreme disturbance scenarios, in terms of 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 had the largest influence on population trends and reproductive parameters for both populations, followed by climate change. Modelling provides insight into how disturbances may affect different population, and so informs management on how best to mitigate their potential effects while there is still time to act.