The effects of low-level aircraft over-flights on behaviour of harlequin ducks (Histrionicus histrionicus) breeding in central Labrador were quantified during 2000–2002. The Canadian Department of National Defence supports a low-level training programme in the 130 000 km2 Military Training Area of Labrador involving military jets. The Institute for Environmental Monitoring and Research (IEMR) undertakes scientific research into environmental impacts of low-level military jet over-flights. A suite of 17 behavioural categories of paired male and female harlequin ducks was modelled, and a canonical variable representing alert behaviour, inactivity on the water and decreased inactivity out of water in response to over-flights represented 73.1% of the variance in the data cluster and provided marked separation of disturbed and undisturbed groups. Behavioural responses of harlequin ducks to military jets were 23 times stronger than their responses to floatplanes, helicopters and military cargo planes, and the significant interaction of aircraft type and noise indicated that noise may be the primary stressor affecting behaviour. A quadratic response of the canonical variable to noise generated from aircraft during standardized 30-minute observation periods was defined. The multivariate analyses were more robust because they indicated covariance in behavioural categories associated with disturbance that was not originally detected in univariate analyses, suggesting the importance of integrating behaviours other than overt responses. The significant effects of military jet over-flights on harlequin duck behaviour emphasize the need to evaluate potential population consequences of aircraft disturbance.