Larvae from the marine medaka fish Oryzias javanicus were exposed with polystyrene microplastics (MPs) for 24 h. Exposure to waterborne fluorescent MPs showed clear ingestion and egestion in feces. Under constant MPs, the concentration of dissolved oxygen significantly decreased in 24 h compared to the control. Significant intracellular reactive oxygen species and malondialdehyde contents were detected in larvae, indicating oxidative stress and lipid peroxidation. Significant elevations in mRNA expressions of heat shock protein 70 and antioxidant defense system genes (glutathione reductase, glutathione peroxidase, catalase, and superoxide dismutase) were measured with increases in enzymatic activity of oxidative stress-related proteins. Taken together, the alterations to the molecular and biochemical components suggested that waterborne MPs had an oxidative stress effect on marine medaka larvae.