Triphenyltin (TPT) is an organotin pollutant widely found in the aquatic environment. It has endocrine-disrupting and osmotic pressure toxicity. In this study, the physiological and biochemical effects of TPT and various salinities were investigated in different tissues (gut, gill, and brain) of marine medaka. The exposure experiments were conducted for 42 days in different salinities (0, 15, and 30 ppt) without TPT exposure and in different salinity groups with TPT exposure concentrations of 100 ng/L, respectively. The results showed that the Na+-K+-ATPase (NKA) and Ca2+ATPase activity had significant tissue-specific differences, with the highest activity observed in the gills, indicating their major contribution to osmoregulation. Changes in salinity also resulted in significant alterations in the ion concentrations of the gut and gill tissues in the 0-C and 15-C groups. While the changes in Na+ and Cl− were relatively stable, the presence of TPT disrupted the regulation of Ca2+ and K+. In conclusion, substantial variations were observed in the osmoregulatory capacity of marine medaka tissues. Environmental concentrations of TPT had little effect on osmotic enzyme activity but interfered with the regulation of Ca2+ and K+ concentrations in the tissues. This study provides valuable insights into the osmotic toxicity of TPT in aquatic environments with different salinities.