Testate amoebae are common inhabitants of moist soils, wetland, and lacustrine habitats. They produce a decay-resistant test, or shell, which can be identified to species in most cases and recovered from sediments in quantities sufficiently large to permit estimation of relative abundance. The objectives of this study were to assess the potential of testate amoeba assemblages as paleoenvironmental and environmental indicators in two Lake Superior coastal wetlands and to determine if morphological variation in four common taxa (Arcella spp., Assulina spp., Centropyxis cassis type, and Nebela tincta-parvula-collaris group) is related to microenvironment. Study localities included ridge-swale wetland systems adjacent to Grand Traverse Bay and Tahquamenon Bay in the Upper Peninsula of Michigan. Testate amoeba assemblages from 74 microsites were compared with percent moisture, depth to water table, pH, porosity, depth of living moss, and associated moss and vascular plant species. Morphometric analysis (e.g., test length and aperture diameter) was conducted on 25 individuals from at least 10 microsites for each of the four selected taxa. Gradient analysis indicated that testate amoeba assemblages are primarily controlled by substrate moisture and pH, consistent with results from other regions. Transfer functions for pH and substrate moisture were developed using ‘jack-knifed’ validation procedures. Little relationship was found between microenvironmental parameters and morphological variation in the investigated taxa, except for the Nebela tincta-parvula-collaris group, where test size was significantly correlated with pH (r² = 0.68). Results indicate that wetland testate amoeba assemblages in these coastal wetland systems are sensitive environmental and paleoenvironmental indicators that can be used to monitor and reconstruct water-level or pH changes.