Hydrological, geomorphological, physicochemical and biological factors influence the nursery function of estuaries. Our study compared the environmental conditions and the assemblages of early life stages of fish in the main four estuaries of the Gulf of Cadiz (Cadiz Bay, Guadalquivir, Odiel-Tinto and Guadiana). Samples were taken within each estuary and on their adjacent coast, during the dry-warm seasons of 2016, 2017 and 2018. Results showed that rivers with smaller basins had a very low freshwater input and their estuaries, Odiel-Tinto and Cadiz Bay, were essentially sea extensions into the land, containing similar physicochemical conditions to nearshore zones, as well as similar assemblages and densities of early life stages of fish. Open water masses of these estuaries do not have important nursery functions. In contrast, inner zones of estuaries with bigger basins and higher freshwater discharges, Guadalquivir and Guadiana, have different environmental characteristics and a long transition zone with a well-defined salinity gradient. Their assemblages and densities of early life stages of fish were different between them and with other estuaries. The Guadalquivir estuary held the highest abundance of larval and early juvenile fish, as well as macrozooplankton biomass. The most abundant fish species in all zones of every estuary was the anchovy Engraulis encrasicolus; the Guadalquivir inner zone had the highest density. High concentration of suspended organic matter, provided by freshwater input and correlated with total suspended solid, suspended inorganic matter and turbidity, was the physicochemical characteristic more typical of the Guadalquivir. This characteristic, in addition to the salinity gradient, could explain the highest densities of macrozooplankton found in this estuary, and consequently, of early fish stages. Recurrent jellyfish blooms were observed in Cadiz Bay and the inner zone of Guadiana, affecting their nursery functions. Odiel-Tinto showed altered physicochemical and biological characteristics, which may need further specific research.