Despite the recognized importance of wetlands as habitat for fishes and the growing need to assess and manage human impacts on that habitat, there is little information on patterns and variability of habitat within Great Lakes coastal wetlands. Our goal was to describe wetland aquatic habitat patterns and the natural factors that organize them as a step towards developing habitat assessment schemes and identifying experimental design elements for future synoptic surveys. We analyzed data on aquatic vegetation structure, water chemistry, and water movement (inferred from gypsum plug dissolution) in relation to hydrology and morphology in inundated segments of ten relatively un-impacted coastal marshes of western Lake Superior. Spatial differences in aquatic habitat within wetlands were as large or larger than differences among wetlands, and habitat patterns were strongly associated with morphology and hydrology. Back-bay segments tended to have greater vegetation cover and structural complexity and lower levels of water movement, and they were prone to high water temperatures and low dissolved oxygen levels in wetlands having little seiche activity. Increasing seiche inputs tended to homogenize habitat elements among wetland segments, while increasing tributary inputs tended to increase spatial variability. Patterns in emergent vegetation differed from patterns in submerged/floating vegetation, and different assessment metrics may be needed for different plant zones. Segment-scale sampling schemes like those used in this study have the potential to elucidate habitat patterns within inundated portions of wetlands with a reasonable level of effort. Human impacts on coastal wetland fish habitat must be interpreted in the context of natural spatial heterogeneity as structured by wetland morphology and magnitude of seiche and tributary inputs.