Pejerrey, Odontesthes bonariensis, is an euryhaline fish of commercial importance in Argentina. This work aimed to determine if water salinity affects the expression of genes involved in somatic growth (gh; ghr-I; ghr-II; igf-I), lipid metabolism (Δ6-desaturase) and food intake (nucb2/nesfatin-1). First, we identified the full-length cDNA sequences of Δ6-desaturase (involved in lipid metabolism) and nesfatin-1 (an anorexigen). Then, pejerrey juveniles were reared during 8weeks in three different water salinity conditions: 2.5g/L (S2.5), 15g/L (S15) and 30g/L (S30) of NaCl. Brain, pituitary, liver and muscle samples were collected in order to analyze mRNA expression. The expression of gh and ghr-II mRNAs increased in the pituitary of fish reared at S2.5 and S30 compared with the S15 group. The expression of ghr-I was higher in the liver of S30 group compared to S2.5 and S15. Igf-I mRNA expression in liver increased with the increment of water salinity, while it decreased in the muscle of S15 and S30 groups. Δ6-desaturase expression increased in S2.5 group compared to S15 in both liver and muscle. S30 caused a decrease in the Δ6-desaturase expression in liver compared to S15. The S30 treatment produced an increase in nucb2/nesfatin-1 mRNA expression in the brain and liver compared to S2.5 and S15. The changes in gene expression observed could help pejerrey perform better during salinity challenges. The S30 condition would likely promote pejerrey somatic growth in the long term.