To understand differences of environmental factors and planktonic communities in closed (CS) versus open (OS) enclosed experimental systems, we performed a study on a 100-L indoor- type artificial marine microcosm. For environmental factors, including water temperature, dissolved inorganic phosphorus, and dissolved silica, there were no significant differences between CS and OS; however, salinity was higher in CS than that of OS due to the evaporation effect. The concentration of dissolved oxygen and dissolved inorganic nitrogen was lower in CS than in OS. The abundance of phytoplankton was lower in CS than in OS. However, abundance of autotrophic nanoflagellates and heterotrophic bacteria varied inversely with that of phytoplankton abundances. In particular, the abundance of heterotrophic nanoflagellates and ciliates increased with bacterial growth after a time lag. Therefore, environmental factors and planktonic communities in CS gradually changed over time and characterized a different artificial ecosystem than in OS.