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Diatoms have been successfully used as indicators of past and present environmental conditions in freshwater and marine habitats, but their diversity and indicative properties in microtidal coastal wetlands of temperate zone are relatively poorly studied. The goal of this study was to determine whether diatoms can be used as indicators of sea level and nutrient content in coastal wetlands of the mid-Atlantic region of the USA. Our exploratory analyses indicated that benthic and marsh soil diatom assemblages were jointly controlled by tidal elevation, salinity, sediment texture, and nutrient content, while the relative importance of these factors varied among datasets targeting different environmental gradients. The habitat type could be correctly inferred from diatom assemblage composition in 79% of samples. A diatom-based model developed for inferring sediment nitrogen content had an average accuracy of prediction of 12.5% of observed nitrogen range. Models for inferring tidal exposure from diatom assemblage data provided assessment with 11–16% accuracy as estimated by the bootstrapped root mean square errors of prediction, which is similar to the accuracy of models based on other microfossils. These results show that despite inherent challenges, such as tidal redistribution of diatom frustules across the intertidal zone, diatoms can be successfully used as an independent source of evidence in paleoreconstructions of sea-level change and nitrogen enrichment, as well as for monitoring current nutrient pollution in mid-Atlantic wetlands.