Changes in stress-associated biomolecules can be used as an important criterion for assessing the levels of environmental pollution because living organisms demonstrate contamination-stimulated stress responses. This study was conducted to determine the environmental status of Masan-Jinhae Bay, Korea, and its effects on marine organisms by investigating the endoplasmic reticulum (ER) dysfunction in the organs of the flat fish, Limanda yokohamae. ER dysfunction was evaluated via Western blot analysis of the ER stress proteins, immunoglobulin heavy chain binding protein (BiP) and C/EBP-homologous protein (CHOP), and the ER stress-associated protein caspase-12. The results showed that the amount of BiP and CHOP immunoreactivity in the flat fish from the bay area was much greater than that from the Gangneung, as a reference site. Similar to the ER stress proteins, the immunoreactivity of caspase-12 was also found to be elevated in the bay area when compared with that of Gangneung. These data suggest that the environmental status of Masan-Jinhae Bay induces the ER stress response, which is able to lead to phenotypic changes in marine organisms including fish.