Inversion of estuaries in the dry tropics (i.e. salinity increases upstream) against the backdrop of a globally changing climate is forcing migratory clupeid fish species to adapt quickly to modifications in their spawning habitats to ensure reproductive success. Hatching success and survival probabilities of marine fish eggs and early life stages are prone to impairment under high temperature and elevated salinity conditions. Essential fatty acids affect osmoregulation in marine fish early life stages, and deficiencies can therefore be expected to cause elevated offspring mortality under hyperosmotic conditions, ultimately modifying a stock's reproductive potential. Here we show that oocytes spawned by bonga shad Ethmalosa fimbriata inside a hypersaline estuary exhibited significantly higher 20:4 (n-6) proportions (1.6 ± 0.7% of total fatty acids) than oocytes spawned under marine conditions (0.6 ± 0.2%). Further, oocyte proportions in 20:4 (n-6), 20:5 (n-3), and 20:6 (n-3) were positively correlated with water temperature, water salinity, and female reproductive investment (relative batch fecundity, gonado-somatic index, oocyte dry weight). Oocytes spawned during high temperature/high salinity conditions inside the estuary are therefore likely to develop normally under the prevailing conditions. Reproductive potential was determined to be highest in females spawning inside the estuary at the end of the wet season, when temperatures are high and salinities are less stressful due to freshwater input. Results lead to the conclusion that migratory clupeid fishes can maintain their reproductive potential in hypersaline estuaries and lagoons, which potentially allows for sustainable stock sizes.