Sedimentary marine habitats are the largest ecosystem on our planet in terms of area. Marine sediment microbiota governs most of the benthic biological processes and therefore are responsible for much of the global biogeochemical activity. Sediment microbiota respond, even rapidly, to natural change in environmental conditions as well as disturbances of anthropogenic source. The later are greatly impact the continental shelf. Characterization and monitoring of the sediment microbiota may serve as an important tool for assessing environmental health and indicate changes in the marine ecosystem. This study examined the suitability of marine sediment microbiota as a bioindicator for environmental health in the Eastern Mediterranean Sea. Integration of information from Bacteria, Archaea and Eukaryota enabled robust assessment of environmental factors controlling sediment microbiota composition: bottom seafloor-depth (representing here sediment grain size and total organic carbon), core depth and season (11%, 4.2% and 2.5% of the variance, respectively). Furthermore, inter- and intra-kingdom co-occurrence patterns indicate ecological filtration as well as stochastic processes may control sediment microbiota assembly. The results show that the sediment microbiota was robust over three years of sampling, in terms of both representation of region (outside the model sites) and robustness of microbial markers. Furthermore, anthropogenic disturbance was reflected by significant transformations in sediment microbiota. We therefore propose sediment microbiota analysis as a sensitive approach to detect disturbances, which is applicable for long-term monitoring of marine environmental health.