Concern for the lack of field studies on the effects of low-level military jet over-flights on wildlife resulted in directed research in the Military Training Area of Labrador, 1999–2002. At Fig River, a tributary of the Lower Churchill River, a before-after-control-impact (BACI) study design quantified effects of aircraft over-flights on behaviour of individual harlequin ducks (Histrionicus histrionicus) in the 130 000 km2 Military Training Area of central Labrador. Noise generated from low-level passes (30–100 m above ground level) by military jets was sudden in onset and high in amplitude (>100 dBA), substantially above background sound levels both at Fig Lake outlet (40–50 dBA) and rapid sections of Fig River (60–70 dBA). Harlequin ducks reacted to noise from military jets with alert behaviour, showing a positive dose-response that especially intensified when noise exceeded 80 dBA. Residual effects, in other words, deviations from normal behaviour patterns after initial responses, were decreased courtship behaviour for up to 1.5 h after, and increased agonistic behaviour for up to 2 h after military jet over-flights. Direct behavioural responses to military jet over-flights were of short duration (generally <1 min), and were unlikely to affect critical behaviours such as feeding and resting in the overall time-activity budgets of breeding pairs. However, the presence of residual effects on behaviour implied whole-body stress responses that were potentially more serious; these require further study because they are potentially more detrimental than immediate responses, and may not be detected in studies that focus on readily observed overt responses. A dose-response curve relating particular behaviours of harlequin ducks to associated noise of over-flights could be a valuable conservation tool for the research and mitigation of environmental impacts of aircraft and other noise.