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ABSTRACT Microbial communities play a fundamental role in biogeochemical cycling within salt and brackish marsh ecosystems, yet fungal‐prokaryotic interactions in these environments remain poorly understood. This study employed metabarcoding of the 16S and 28S rRNA genes to investigate prokaryotic and fungal communities across four locations in sediments and surface waters of the North Inlet salt marsh and Winyah Bay brackish marsh (South Carolina, USA) over four time points from 2020 to 2021. Co‐occurrence network analyses were used to identify potential microbial interactions and their ecological implications. Distinct fungal and prokaryotic communities were observed between the two marsh types. From the 16S prokaryotic primer set, Proteobacteria, Bacteroidota, and Cyanobacteriota dominated both marshes. Early diverging fungi and Actinomycetota (bacteria) were prevalent in the brackish marsh, whereas salt marsh communities were primarily composed of Dikarya fungi (Ascomycota and Basidiomycota) and Desulfobacteria. Network analyses revealed contrasting interactions between surface water and sediment. In brackish marsh sediments, fungi and prokaryotes exhibited nearly exclusively negative connections, suggesting strong resource competition. In contrast, Dikarya fungi in brackish marsh surface water displayed numerous positive connections with bacteria, suggesting potential cross‐feeding interactions. In the salt marsh, fungi and prokaryotes exhibited potential cooperative and competitive/antagonistic interactions. Ascomycota were positively connected with Desulfobacteria, suggesting a role in complex organic matter degradation. Conversely, negative connections between Chytridiomycota (early diverging fungi) and Cyanobacteriota (bacteria) implied parasitic interactions. These findings highlight the dynamic nature of fungal‐prokaryotic interactions in coastal ecosystems. By analyzing potential microbial relationships in salt and brackish marshes, this study provides new insights into the ecological roles of fungi in estuarine environments, particularly their contributions to nutrient cycling and organic matter decomposition. Understanding these interactions is crucial for generating hypotheses and predicting microbial responses to environmental changes—such as shifts in salinity and nutrient availability—and their potential impacts on marsh ecosystem functioning.