Understanding processes governing coastal erosion is becoming increasingly urgent because highly valued ecosystems like salt marshes are being lost at accelerating rates. Here we examine the role of biotic interactions in mediating marsh shoreline erosion under wind wave forces. We parameterized analytical and cellular automata models with field data to assess how soil heterogeneity among clonal patches of an ecosystem engineer mediates spatiotemporal patterns of marsh shoreline erosion. We found that spatial heterogeneity accelerates erosion, especially when it is organized in patches of intermediate size. Patch size also mediated interannual variability in erosion and strongly controlled shoreline roughness. Our results indicate that shoreline roughness can be diagnostic of internal biological structure and spatiotemporal variability in erosion. Hence, measures of shoreline roughness may inform the timeframe and spatial extent needed to accurately monitor erosion. These findings highlight how the physical response of marsh shorelines to wind wave erosion is a function of landscape ecology. Plain Language Summary Understanding processes governing coastal erosion is becoming increasingly urgent as highly valued ecosystems like salt marshes are being lost at accelerating rates. This paper investigates how marsh shoreline erosion is affected by the spatial composition of clonal plants. Plant “engineer” species are known to increase soil shear strength, decreasing rates of erosion. Consequently, phenotypic variation among clonal individuals may affect shoreline erosion. Because erosion proceeds as an advancing front, it may be influenced by how soil resistance is spatially organized. We found that, while random variation increased erosion rates, the effect was stronger when variation was organized into clonal patches—particularly ones that were intermediately sized. With increasing clone size, shoreline shape became rougher, and the variability of annual erosion rates increased. Not only does this highlight how a physical process is shaped by biotic attributes, it also shows how the resulting shoreline shape may be diagnostic of biological structure and influence. Key Points Analytical and simulation models show the role of biogeomorphic heterogeneity in mediating marsh shoreline erosion under wind wave forces Acceleration of marsh erosion is greatest when soil spatial heterogeneity is organized by clonal vegetation patches of intermediate size The variability of annual erosion rates and roughness of marsh shorelines increase with the size of clonal vegetation patches