Chronic effects such as reproduction and population dynamics with elevated $CO_2$ concentration were evaluated using two representative marine benthic species, copepod (Tisbe sp.) and amphipod (Monocorophium acherusicum) adopting long-term exposure. Juvenile copepod and amphipod individuals were cultivated in the seawater equilibrated with control air (0.395 mmol $CO_2$/air mol) and high $CO_2$ air having 0.998, to 3.03, 10.3, and 30.1 mmol $CO_2$/air mol during 20 and 46 days, respectively. After the exposure period, the number of benthic invertebrate was counted with separate larval and juvenile stage such as naupliar, copepodid and adult for copepod, or neonate and adult for amphipod, respectively. The individual number of both test species at each life-stage was significantly decreased in seawater with 10.3 mmol $CO_2$/air mol or higher. Recently, the technology of marine $CO_2$ sequestration has been developed for the reduction of $CO_2$ emission, which may cause climate change. However, under various scenarios of $CO_2$ leaks during the injection process or sequestrated $CO_2$ in marine geological structure, the potential risk to organism including various invertebrates can be expected to exposure. So the results of this study suggested that the detailed consideration on the adverse effect with marine ecosystem can be prerequisite for the marine $CO_2$ sequestration projects.