The giant mud crab (Scylla serrata) is an important fisheries species throughout southeast Asia and the South Pacific. In Australia, marine protected areas (MPAs) and fish habitats have been declared specifically to protect the local populations of S. serrata. The cannibalistic behaviour of S. serrata coupled with the potential attraction of increased predators may counteract the effect of excluding fishing from these areas as a means of increasing the local crab population. The population dynamics of S. serrata could also be confounded by the spatio-temporal variability in environmental conditions (e.g. run-off and temperature). Here, we used a spatially explicit individual-based model (IBM) to explore the population dynamics of S. serrata in an MPA located in southern Moreton Bay, Queensland, Australia. This IBM simulated the life cycle dynamics of individual S. serrata and integrated the key processes affecting its population dynamics. These processes include physical transport of the planktonic life stages, movement, growth, metamorphosis, setting, reproduction, spawning, harvesting, and predation. Individual variability was built into the model to account for demographic variation. The modelled scenarios indicated that the effect of the different harvest strategies trialled on the population dynamics after 30 months and the MPA influenced the number of individuals in the creek system resulting in a partial 35% population increase. Further development and application of this model has implications for MPAs and catch limits under multiple stressors including climate change.