Many important wetland functions are tied to sediment dynamics, which are influenced by infaunal invertebrate communities. These communities are sensitive to changes in sediment structure and to colonization by non-native species. In a southern California salt marsh, the non-native isopod Sphaeroma quoianum has created dense networks of burrows within the marsh banks. Since this isopod increases erosion in many areas and can change local invertebrate communities, its possible contribution to habitat loss in this already-scarce southern California ecosystem is an important issue. To determine the relationship of S. quoianum to invertebrate community and sediment characteristics, three burrowed transects and one unburrowed transect were surveyed and sampled for invertebrate and sediment cores. This study tested the association between burrows and grain size distribution, sediment carbon content, respiration rates, and invertebrate community composition. Sphaeroma quoianum burrows were correlated with altered invertebrate community composition, decreased carbon content, and steep marsh bluffs. These results highlight the potential susceptibility of salt marsh habitat with steep edges to invasion by non-native species. These results also suggest that S. quoianum invasion of salt marsh habitats can alter native communities and ecosystem functions; thus, incipient invasions should be of concern to managers and ecologists alike.