Patterns in the Southern Oscillation Index (SOI) affect the life history of many aquatic organisms in the southern hemisphere. We examined the effect of this phenomenon and other factors (i.e. rainfall, river flow and sea surface temperature, SST) on the commercial harvest of the giant mud crab (Scylla serrata) in Australia, given the large inter-annual variations in the catch of this species over the last 15 years, particularly in the north. Regression models were applied to concurrent environmental and catch data for giant mud crab caught from 29 catchments that provided a combined harvest of >20 000 tonnes. Non-metric multidimensional scaling (nMDS) was also used to explore potential regional differences in catch trends. A combination of SOI, SST and rainfall/river flow explained 30–70% of the variability in commercial catches, with mean summer temperature being most influential at higher latitudes. The nMDS revealed distinct groupings of river systems that coincided with biogeographic regions. This work highlights the importance of climatic events on the harvest of giant mud crabs and reinforces the need to adopt a bioregional approach when assessing the performance of fisheries targeting this species.