The fish assemblage of the Óbidos lagoon was studied between January 1993 and December 1994 based on beach seine catches. Forty-one species were identified, with Gobius niger, Syngnathus acus, Atherina boyeri, Dicentrarchus labrax, Liza aurata, Chelon labrosus and Symphodus bailloni the most common species. The community was dominated by the families Atherinidae, Mugilidae and Gobiidae, which is characteristic of temperate and tropical estuaries and coastal lagoons. Community ordination analysis outlined three major fish assemblages along a longitudinal environmental gradient, determined by salinity, sediment and turbidity. Euryhaline fish species, such as Liza ramada and Mugil cephalus, were particularly abundant in the upper part of the lagoon. The middle area was dominated by estuarine resident species, namely G. niger, A. boyeri, S. acus and S. bailloni, while in the lower part of the lagoon the fish assemblage was composed of inshore marine species. The seasonal pattern was mainly induced by the annual cycle of resident species and by the migration of juveniles moving between coastal areas and the lagoon. If human activities related to keeping the mouth of the lagoon open to the sea ceased, the nursery function of this estuarine system would be affected, with a dominance of euryhaline fish species expected throughout the lagoon.