The expansion of urban and agricultural activities in watersheds of the Midwestern USA facilitates the conversion of species-rich sedge meadows to stands of Phalaris arundinacea and Typha spp. We document the role of sediment accumulation in this process based on field surveys of three sedge meadows dominated by Carex stricta, their adjacent Phalaris or Typha stands, and transitions from Carex to these invasive species. The complex microtopography of Carex tussocks facilitates the occurrence of other native species. Tussock surface area and species richness were positively correlated in two marshes (r² = 0.57 and 0.41); on average, a 33-cm-tall tussock supported 7.6 species. Phalaris also grew in tussock form in wetter areas but did not support native species. We found an average of 10.5 Carex tussocks per 10-m transect, but only 3.5 Phalaris tussocks. Microtopographic relief, determined with a high-precision GPS, measured 11% greater in Carex meadows than Phalaris stands. Inflowing sediments reduced microtopographic variation and surface area for native species. We calculated a loss of one species per 1000 cm² of lost tussock surface area, and loss of 1.2 species for every 10-cm addition of sediment over the sedge meadow surface. Alluvium overlying the sedge meadow soil had a smaller proportion of organic matter content and higher dry bulk density than the buried histic materials. We conclude that sedimentation contributes to the loss of native species in remnant wetlands.