Mesocosms are real-world environmental science tools for bridging the gap between laboratory-scale experiments and actual habitat studies on ecosystem complexities. These experiments are increasingly being applied in understanding the complex impacts of heavy metals, ocean acidification, global warming, and oil spills. The insights of the present review indicate how metals and metal-bound activities impact on various aspects of ecological complexities like prey predator cues, growth, embryonic development, and reproduction. Plankton and benthos are used more often over fish and microbes owing to their smaller size, faster reproduction, amenability, and repeatability during mesocosm experiments. The results of ocean acidification reveal calcification of plankton, corals, alteration of pelagic structures, and plankton blooms. The subtle effect of oil spills is amplified on sediment microorganisms, primary producers, and crustaceans. An overview of the mesocosm designs over the years indicates that gradual changes have evolved in the type, size, design, composition, parameters, methodology employed, and the outputs obtained. Most of the pelagic and benthic mesocosm designs involve consideration of interactions within the water columns, between water and sediments, trophic levels, and nutrient rivalry. Mesocosm structures are built considering physical processes (tidal currents, turbulence, inner cycling of nutrients, thermal stratification, and mixing), biological complexities (population, community, and ecosystem) using appropriate filling containers, and sampling facilities that employ inert materials. The principle of design is easy transportation, mooring, deployment, and free floating structures besides addressing the unique ecosystem-based science problems. The evolution of the mesocosm tools helps in understanding further advancement of techniques and their applications in marine ecosystems.