Shoreline armoring is an ancient and globally used engineering strategy to prevent shoreline erosion along marine, estuarine, and freshwater coastlines. Armoring alters the land water interface and has the potential to affect nearshore submerged aquatic vegetation (SAV) by changing nearshore hydrology, morphology, water clarity, and sediment composition. We quantified the relationships between the condition (bulkhead, riprap, or natural) of individual shoreline segments and three measures of directly adjacent SAV (the area of potential SAV habitat, the area occupied by SAV, and the proportion of potential habitat area that was occupied) in the Chesapeake Bay and nearby Atlantic coastal bays. Bulkhead had negative relationships with SAV in the polyhaline and mesohaline zones. Salinity and watershed land cover significantly modified the effect of shoreline armoring on nearshore SAV beds, and the effects of armoring were strongest in polyhaline subestuaries with forested watersheds. In high salinity systems, distance from shore modified the relationship between shoreline and SAV. The negative relationship between bulkhead and SAV was greater further off shore. By using individual shoreline segments as the study units, our analysis separated the effects of armoring and land cover, which were confounded in previous analyses that quantified average armoring and SAV abundance for much larger study units (subestuaries). Our findings suggest that redesigning or removing shoreline armoring structures may benefit nearshore SAV in some settings. Because armoring is ubiquitous, such information can inform efforts to reverse the global decline in SAV and the loss of the ecosystem services that SAV provides.