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Both seagrasses and bivalve shellfish provide valuable ecosystem services in estuaries worldwide. Seagrasses are protected by no-net-loss provisions in US federal and state regulations, resulting in precautionary management that avoids any direct impacts from development activity, including shellfish aquaculture. Recent research suggests that oyster aquaculture has direct impacts on native seagrass (eelgrass Zostera marina) at small spatial and short temporal scales in US west coast estuaries. We quantified impacts of oyster aquaculture on Z. marina at the estuarine landscape scale in Willapa Bay, Washington. A model of Z. marina cover outside of aquaculture was created using distance to estuary mouth, distance to nearest channel, salinity, elevation, and cumulative wave stress as factors, and was then used to predict Z. marina distribution within oyster aquaculture beds and compared to an inverse distance interpolation of points outside of aquaculture. The amount of Z. marina cover observed within oyster aquaculture beds was less than predicted, but represented <1.5% of the total predicted amount of Z. marina cover in Willapa Bay in any year. Type of oyster culture bed did not contribute to observed variation, but mechanically harvested beds had significantly less Z. marina cover than beds harvested by other methods. The majority of beds had 65−145% of the model-predicted Z. marina cover and exhibited relatively low variability between years, suggesting that Z. marina as habitat is resilient to oyster aquaculture as a disturbance and does not result in persistent effects at the landscape scale in this estuary.