Hypoxia (dissolved oxygen < 2 mg L–1) has emerged as a worldwide threat to coastal and estuarine ecosystems. Beyond direct mortality, secondary ecological impacts caused by hypoxia-driven distributional shifts may be equally important. From July–November 2009 and June–September 2010, we quantified the movement patterns of Dungeness crab (Metacarcinus magister) and English sole (Parophrys vetulus) in Hood Canal, Washington USA, a seasonally hypoxic estuary. Although highly mobile (mean cumulative distance ± SD = 11.0 ± 25.6 km, N = 60), there was little evidence of either species exhibiting large-scale directional movement out of the hypoxic region. However, Dungeness crab showed significant shifts towards shallower waters and elevation in activity in the hypoxic region, potentially increasing their vulnerability to crabbing and other indirect ecological consequences. Our findings suggest hypoxia could have a more localized impact on the mobile fauna in Hood Canal. However, more detailed information concerning the local-scale oxygen dynamics and responses of these species, such as English sole vertical movement, is essential for grasping the population and community level effects of hypoxia.