Objective: Gotjawal refers to a special geographical designation found in Jeju Province, Korea, where vegetation forms over a rocky area. Due to the important ecological value of Gotjawal, international concern about such areas is growing. However, only limited information is available regarding environmental contamination of Gotjawal. This study was conducted in order to investigate the levels of contamination and associated ecotoxicological effects of surface water bodies in Gotjawal. Methods: Surface water samples were collected at three sampling sites in two Gotjawal areas and were analyzed for several pharmaceuticals and pesticides in consideration of the potential sources of contamination. The ecotoxicity of the samples was measured using water fleas (Daphnia magna and Moina macrocopa) and zebrafish (Danio rerio). In addition, effects on the gene transcription of zebrafish were investigated following exposure to the samples. Results: Nine pharmaceuticals were detected in the samples, but none of the target pesticides were detected. Following acute exposure to two surface water samples, the survival of waterfleas was significantly reduced, but reproduction was not affected. In zebrafish, time-to-hatch was delayed and fry survival was decreased in some samples. On the other hand, at the transcriptional level, there were no genes significantly influenced by exposure to the samples. Conclusion: This is the first study investigating environmental contamination in Gotjawal areas and associated ecotoxicities. Further studies are warranted to identify the cause of acute Daphnia toxicity and to determine potential consequences of longer-term exposure in Gotjawal areas.