The predictive accuracy of complex fisheries models developed to anticipate the effects of changing fishery regulations appears to depend on a solid understanding of the processes and feedback systems linking biological and physical information to resource user. Many fisher decisions are modelled in the human component of the models, including inertia, or location choice flexibility. We unpack a whole of ecosystem system model and explore how location choice flexibility in fleet behaviour (sticking to the same seasonal and spatial distribution of fishing) affects outcomes such as catches and income levels and variability. Our analysis shows that the interpretation is not straightforward, and the relationship between behavioural flexibility and income level and income variability has to be considered in the context of three main fleet characteristics: profitability; how diversified the fleet is; and growing or declining target species biomass. We contend that making behavioural flexibility sensitive to the health of the stock and fleet profitability could potentially improve accuracy of large whole of ecosystem models such as Atlantis.