Fish larvae were collected monthly between March and September 1997 in the Mira and Guadiana estuaries (southern Portugal). Hydrological parameters were registered and zooplankton samples were obtained simultaneously. Densities of fish larvae (ind·100 m–3) were calculated from 211 samples and larval nutritional condition measured as RNA/DNA ratios were obtained for 346 individuals, using a fluorimetric method for nucleic acid quantification. Correlating variables were further studied using multiple regression analysis in order to assess the relative importance of abiotic and biotic factors affecting within-year trends in abundance and nutritional condition of estuarine fish larvae. Results indicated that: 1) the abundance of fish larvae seems conditioned by temperature and predation; and 2) their nutritional condition is dependent on temperature and prey availability. Temperature is an important variable structuring estuaries and therefore conditions the behaviour and physiology of fish larvae. Furthermore, the co-occurrence of predators and larvae might be related to similar feeding patterns or comensalism. Whenever feeding conditions are suitable, they usually determine enhanced growth and nutritional condition. However, predation seems to control this latter relationship through its effect on larval mortality.