The current growth of nano-industries has resulted in released nanoparticles entering into water and soil ecosystems via various direct or indirect routes. Physicochemical properties of nanoparticles differ from bulk materials, and nanomaterials influence the fates of nanoparticles and the interactions of living or non-living things in the environment. Microcosm analysis is a research methodology for revealing natural phenomena by mimicking part of an ecosystem under controlled conditions. Microcosm study allows for the integrated analysis of toxic effects and fates of nanoparticles in the ecosystem. Ecotoxicity studies of nanomaterials are steadily increasing, and microcosm studies of nanomaterials are currently beginning to surface. In this study, microcosm studies of nanomaterials in water and soil ecosystems were extensively investigated based on SCI(E) papers. We found that the microcosm studies have been reported in 12 instances, and mesocosm studies have been reported in only once until now. Advanced research was mostly evaluated at the microorganism level. But integrated analysis of nanotoxicity is required to research the interactions based of various species. Thus, our studies analysed the trend of microcosm studies on nanomaterials in water and soil ecosystems and suggested future directions of microcosm research of nanomaterials.