The relative importance of nursery areas and their relationships with several environmental variables were evaluated in nine estuarine systems along the Portuguese coast based on trawl surveys. Historical data were used to outline changes and trends in the nursery function of some of these estuaries over the past decades. The dominant flatfish species in Portuguese estuaries were Platichthys flesus (Linnaeus, 1758), Solea solea (Linnaeus, 1758), Solea senegalensis Kaup, 1858 and Monochirus hispidus Rafinesque, 1814, but their occurrence differed among the estuaries. P. flesus only occurred in estuaries north of the Tejo estuary (39°N), S. solea was quite rare along the southern Portuguese coast (south of 37°30′N), S. senegalensis occurred in estuaries throughout the coast, but its abundance varied considerably, and the occurrence of M. hispidus was limited to the Sado estuary and Ria Formosa. A Correspondence Analysis was performed to evaluate the relationships between flatfish species abundance and geomorphologic and hydrologic characteristics of estuaries (latitude, freshwater flow, estuarine area, intertidal area, mean depth and residence time). Abiotic characteristics (depth, temperature, salinity, sediment type) of nursery grounds of each flatfish species were also evaluated. Results showed that some estuaries along the Portuguese coast have nursery grounds used by several flatfish species (e.g. Ria de Aveiro, Sado estuary), while in other systems a segregation was noticed, with juveniles of different species occurring in distinct estuarine areas (e.g. Minho and Mondego estuaries). This emphasizes the relevance of niche overlap, but the potential for competition may be considerably minimized by differences in resource use patterns and by an extremely high abundance of resources. Peak densities of flatfishes recorded in nurseries areas along the Portuguese coast were within the range of values reported for other geographical areas. Inter-annual abundance variability of all the species in the Tejo and Sado estuaries was extremely high, with a drastic decrease in P. flesus in the Tejo estuary, probably related to higher water temperature in recent years due to global climate change.