Mud crabs (Scylla spp.) are a high value commodity harvested in the Indo-West Pacific. Scylla species support important artisanal fisheries in south-east Asia and intensive commercial fisheries in Australia where the market demand and catch has increased markedly over the last decade. Over-fishing of Scylla spp. has been observed at varying levels throughout its distribution. Fluctuations in catch rates and abundance are thought to be driven by climate parameters. Here we analyse monthly, seasonal and annual patterns in catch and effort data (from 1990 to 2008) for the commercial giant mud crab (Scylla serrata) fishery in the Northern Territory, Australia, with corresponding climatic data (rainfall, freshwater runoff, sea surface temperature) and the Southern Oscillation Index (SOI) as an indicator of La Niña/El Niño events. Between 30 and 40% of the variation in catch per unit effort can be explained by rainfall and SOI alone. This result was supported by linear mixed models which identified SOI as the main contributor to the model. Spectral analyses showed that catch peaks coincided with a four year La Niña cycle. One- and two-year time lags (consistent with S. Serrata’s life cycle) were also significantly correlated to SOI values and rainfall. These outcomes may assist fishery managers in planning fishing exposure period and duration. Furthermore, findings of this study provide information on the vulnerability of S. serrata to fluctuations in environmental conditions and can help to apply protective measures when and where necessary.