We explored to what extent morphological variation and habitat modification are correlated for an autogenic ecosystem engineer, which is an organism that modifies its habitat via its own physical structures. The intertidal salt marsh species Spartina anglica is well known for its capacity to enhance sediment accretion within its canopy by reducing hydrodynamic energy. Sediment accretion is favorable to Spartina, as it reduces inundation stress, enhances soil drainage, and enhances nutrient availability. Shoot density and clonal architecture showed a large variation that was strongly correlated with the marsh elevation and sediment type. This correlation showed that at the lowest elevations at the muddy site, Spartina tussocks had the highest shoot density, which is known to be favorable for sediment accretion by reduction of hydrodynamic energy. There was also a strong positive correlation between the amount of sediment that accumulated within a tussock and gully formation around that Spartina tussock. The tussocks at the lowest elevations at the muddy site had the lowest lateral tussock growth. At the highest elevations at the sandy site, stem densities were lower and there was a relatively high rate of clonal expansion and marsh formation. At this location, we also observed tussock mortality due to erosion of several of these openly structured tussocks. Based on the observed correlations, we hypothesize that the morphology of Spartina represents trade-offs between the capacity to maximize habitat modification through sediment trapping by having a high shoot density versus the capacity to maximize clonal expansion by spreading shoots widely and the capacity of maximal clonal expansion by spreading shoots widely versus the risk of tussock mortality due to insufficient modification of the habitat that makes the tussock vulnerable to erosion. Our results indicated that morphological variation and habitat modification are strongly correlated for the autogenic ecosystem engineer S. anglica.