Planktonic organisms has a close relationships with the environmental change in water column. As such, application of plankton is an effective approach to develope biological tools for the marine ecosystem health assessment. Major issue between coastal pollution and plankton has been usually recognized on the phytoplankton bloom or red tide caused by the eutrophication of inorganic nutrients. However, overall pollution effect on the planktonic communities should be simultaneously considered with the organic pollutants as well as the inorganic nitorgen and phosphate. Among the various planktonic taxa, heterotrophic bacteria, heterotrophic flagellates, and ciliates which are major components within the microbial loop should be investigated to understand the organic pollution effect. Generally, there are three ways to evaluate the marine environment based on the plankton community. First, community basis approaches such as diversity index and chlorophyll concentration are common tools in the plankton analysis. Especially chlorophyll concentration has been applied for evaluating the water quality from many countries. Second, bioassessment approach in the species level is one method of monitoring the pollution indicative species. For the application of the second approach, the species identification should be an essential work. Third, toxicological tests can be applied to the planktonic organisms in a standard bioassay. A case study in Masan Bay would be an available assessment to combine the two effects from inorganic and organic pollution. A new approach using plankton communities was tentatively suggested as a biological tool to evaluate the ecosystem health in Masan Bay.