The frequency of seasonal and short-term hypoxia is increasing in coastal seas. How such repeated disturbances affect key species that have important roles for ecosystem processes and functions remains, however, unknown. By performing a field experiment we explored if the bivalve Macoma balthica can cope with short-term, recurring hypoxic stress, and investigated how hypoxia affects the condition of surviving bivalves. By combining data on different levels of biological organization, i.e., on physiology (biomarker response), behaviour and demography, we identified stress responses before the population declined. One pulse of hypoxic disturbance (3 days) resulted in behavioural alterations, as adult M. balthica extended their siphons, emerged towards the sediment surface and expressed decreased reburial rates. However, the demographic structure of the population remained unaltered. Several pulses of recurring hypoxic stress resulted in physiological response with changes in glutathione reductase and acetylcholinesterase enzyme activities. The recurring hypoxic disturbance was observed to affect juvenile bivalves before adults, while pro-longed hypoxia reduced the entire bivalve population. Our results clearly show that hypoxic stress changes the behaviour and physiology of M. balthica before demographic changes occur, which is likely to have severe implications for the contribution of this key species to ecosystem functioning. That a combination of measures at different levels of organization can detect disturbances at an early stage suggests that such an approach would be useful for assessing the effects of disturbances on marine ecosystems that are increasingly affected by anthropogenic change.