Estuary perch, Macquaria colonorum, is a truly estuarine species and spawns naturally in salt-wedged estuaries in salinities of 20–30. In this study, results on the changes in the total amino acids (TAA) (protein bound + free) and free amino acid (FAA) pools of developing eggs and newly hatched larvae until yolk-sac resorption were evaluated at four incubation salinities (15, 20, 25 and 30). The TAA in 1-h post-fertilised eggs ranged from 207.4 ± 2.2 to 231 ± 10 nmol·egg–1, at salinities of 20 and 15, respectively. The TAA content decreased significantly (P < 0.05) as development progressed. The FAA in eggs of estuary perch ranged from 35.5 ± 0.5 to 41.0 ± 0.9 nmol·egg–1 at salinities of 30 and 15, respectively, and accounted for 15.7–28.0 % of the TAA. In newly hatched larvae the TEAA accounted for between 42.0 and 43.2 % of the TAA. The FAA decreased significantly with development, it being reduced in yolk-sac resorbed larvae to 19, 16.2, 22.8 and 28.7 % of that of the original amount in fertilised eggs in salinities of 15, 20, 25 and 30, respectively. The FEAA in the FAA pool also decreased significantly with development, to approximately 33.7–35.3 % in yolk-sac resorbed larvae from that in fertilised eggs. The data suggest that estuary perch uses its FAA for energy dissipation during early ontogeny rather than for body protein synthesis. Overall, the amino acid profiles of estuary perch were close to that of pelagic eggs of marine fish, and there were no major influences of salinity on the amino acid profiles as development progressed.