Infestation by introduced zebra mussels has extirpated native unionids in many Great Lake habitats. Shallow areas in coastal wetlands are intermittently dewatered by seiches and seasonal water level changes, and we examined how water level fluctuations and sediment characteristics affected interactions among unionids and zebra mussels in a Lake Erie coastal marsh. In 2001 we sampled unionid distributions and measured zebra mussel colonization on PVC plates at 1 cm, 18 cm and >35 cm water depths. We found a diverse unionid community (15 species) with many juvenile unionids. Unionid densities (0.01 unionids/m²) were comparable to other coastal wetlands, but are lower than reported in offshore areas before zebra mussels were introduced. Zebra mussels colonized plates at >3000 individuals/m² in some locations. Although >60% of unionids had byssal threads on their shells, >75% of unionids had no attached zebra mussels. Therefore, zebra mussels are colonizing unionids, but are not surviving. Unionid numbers and zebra mussel colonization were low in shallow (1–35 cm) water depths, indicating that water level fluctuations limited their distributions. Only two species of unionids were collected in 1–17 cm deep areas, and areas that became mudflats in September had almost no unionids. Numbers of zebra mussels and unionids were not correlated with organic content or silt/clay content of the sediments. Habitat characteristics shared by this wetland and other coastal wetlands that are important refuges of unionids include: a hydrological connection with the lake, areas deep enough for unionids to survive low water levels and soft sediments that allow unionid burrowing.