The presence of bivalves and bivalve aquaculture can have positive and negative impacts on seagrass and associated benthic communities. Some oyster (Crassostrea gigas) aquaculture methods recently have been restricted to reduce benthic disturbance and protect native eelgrass (Zostera manna) in West coast (USA) estuaries. We argue that aquaculture, like all food production systems, involves tradeoffs with natural systems, but that the magnitude of those tradeoffs depends on the ecological details of the production system. Capitalizing on oyster aquaculture farms as large scale “manipulations” in Willapa Bay, WA (USA), we explored three different oyster aquaculture methods (mechanical harvest or “dredged” on-bottom, hand-picked on-bottom and long line off-bottom). We found that both the biological (oyster-eelgrass interactions) and physical (disturbance or structure) components of aquaculture led to changes in the eelgrass population. Eelgrass density declined with oyster density in all aquaculture areas, likely as a result of direct competition for space. Eelgrass relative growth rate, plant size, and production did not change with oyster density. However, all eelgrass measures were affected by aquaculture, and the type and magnitude of impacts varied among eelgrass measures and aquaculture methods. Throughout the bay, eelgrass in long line areas occurred at densities indistinguishable from nearby uncultivated areas, but in 2004, eelgrass in long line areas was smaller (32%) and had lower production per area (70%). Cultivating oysters in dredged or hand picked beds increased eelgrass growth rates slightly, but led to lower eelgrass density (70% and 30%, respectively), plant size (32%, both cases), and production (70%, both cases). In a large scale simulated mechanical harvest experiment, the temporal response of eelgrass density varied dramatically by site, ranging from 1 to >4 y. If eelgrass impact reduction, rather than avoidance, is identified as the management goal, the degree of tradeoff between eelgrass habitat and oyster production can be minimized by managing aquaculture methods or oyster planting densities, depending on the eelgrass measure of interest. Explicit management goals and appropriate eelgrass habitat indicators must be developed before our findings can be used to suggest best management practices for intertidal aquaculture in the Pacific Northwest.