Environmental changes (a type of disturbance) are altering the habitat of southern elephant seals Mirounga leonina, an apex marine predator in the Southern Ocean. As a result, individuals may shift their behaviour, spending more time in transit and less time foraging. The effects of these sublethal changes in behaviour can accumulate, indirectly impacting lifetime fitness through changes in individual survival and reproduction. If a sufficient proportion of the population is affected, the probability of population persistence will be altered. We used data from long-term telemetry studies of female elephant seals at Macquarie Island, Australia, to model the effect of behaviour on the seals’ health (i.e. all internal factors that affect homeostasis). Through simulation, we investigated the effect of increasing periods of behavioural shifts, quantifying how the exclusion of maternal southern elephant seals from foraging habitat may affect their health, offspring survival, individual fitness and population growth rate. A long period of altered behaviour (>50% of an average foraging trip at sea) in 1 yr resulted in a small (0.4%) decline in population size the following year. However, a persistent disruption (e.g. 30 yr), caused for example by the long-term effects of climate change, could result in a 0.3% decline in individual fitness and a 10% decline in population size. Our approach to estimating the long-term population effects of short-term changes in individual behaviour can be generalised to include physiological effects and other causes of behavioural and physiological disruption, such as anthropogenic disturbance, for any species.