Estuarine environments accumulate large quantities of organic matter from land masses adjoining the sea, and this is consumed as part of the detritus cycle. These environments are rich in biodiversity, and their ecosystem services greatly benefit humans. However, the estuarine environments have complicated aqueous ecosystems, thus the comprehensive evaluation of biotic interactions and stability is difficult using conventional hypothesis-driven approaches. In this study, we describe the advancement of an evaluation strategy for characterizing and visualizing the interactions and relationships among the microorganisms and chemicals in sediment ecosystems of estuarine environments by a combination of organic matter and elemental profiling as well as microbial profiling. We also report our findings from a comparative analysis of estuarine and coastal environmental samples collected from the Kanto and Tsunami-affected Tohoku regions in Japan. The microbial-gated correlation deployed from the coefficient of microbiota from the correlation matrix and network analysis was able to visualize and summarize the different relationships among the microbial communities, sediment organic matter, and element profiles based on geographical differences in Kanto and Tohoku regions. We demonstrated remarkable estuarine eutrophication in the Kanto region based on abundant sediment polypeptide signals and water nitrogen ions catabolized by microbiota. Therefore, we propose that this data-driven approach is a powerful method for analyzing, visualizing, and evaluating complex metabolic dynamics and networks in sediment microbial ecosystems and can be applied to other environmental ecosystems, such as deep sea sediments and agronomic and forest soils.