Increases in the frequency and duration of hypoxia and the loss of biogenic reefs are two of the most prominent environmental insults to estuaries. We investigated the interaction between moderate hypoxia and habitat restoration activities on estuarine ecosystems by measuring population growth and somatic growth for newly settled Eastern oysters (Crassostrea virginica). Experiments were conducted at a site that historically experiences moderate hypoxia (2.0 mg l^-1 < [O₂] < 4.0 mg l^-1) (Whitehouse Reef) and at a site that experiences normoxia (Dauphin Island). Panels with known starting densities of oyster spat were deployed at the surface, 1.25 m above the bottom, and 0.5 m above the bottom at both sites. Population growth at the bottom and the 1.25 m panels at Whitehouse Reef was -1% to 0% individuals day^-1 caused by periods of moderate hypoxia; however, as oxygen conditions improved in September, population growth increased to approximately 1 to 3% individuals day^-1. For these two panels, total population growth averaged 1% over the experiment duration. For the surface panel at Whitehouse Reef and all three depths at Dauphin Island, population growth remained positive with population growth of between 2% to 17% individuals day^-1. Somatic growth indicated significant location and depth specific differences with somatic growth being negatively correlated with depth. Marginal water quality caused by moderate hypoxia may limit oyster population growth to a much greater extent than predicted by previous laboratory experiments. Additionally, we demonstrate that low-cost experiments prior to the initiation of restoration activities can help ensure success by providing critical in situ information on design and location.