Short-term dynamics in juvenile fish assemblage structure were studied to test whether the most abundant species show temporal segregation, in order to assess whether selected environmental variables could predict species groupings, and to examine the stability of sunset–day–sunrise–night differences. Samplings were collected at 3-h intervals over 48 h on a seasonal basis between spring 2005 and winter 2006. Fish species richness and abundance were higher in spring, and the lowest values occurred in winter. Harengula clupeola occurred mainly in spring, whereas Atherinella brasiliensis peaked in summer and autumn. On the other hand, Trachinotus carolinus, Umbrina coroides and Mugil liza were abundant in winter. Although temperature, salinity and dissolved oxygen were not found to have a strong effect on the abundance patterns of most species, they did appear to have a significant influence on assemblage groupings, according to canonical correspondence analysis and Spearman rank correlation. There is no consistency of diel usage patterns by a given species across seasons. The relative abundance differed between the time of day, which differed among the seasons; this further complicates an understanding of the dynamics of an assemblage. Studies of diel changes that pooled the sampling period as day or night can miss important changes that occur in a short time scale, such as a 3-h period.