In Caeté Estuary, the decrease of larval abundance downstream was attributed to reduced retention, since ebb tide densities prevailed mainly in the middle and lower estuary during the rainy season due to increased freshwater outflow. Anchovia clupeoides, Stellifer microps and Guavina guavina were most abundant in the late dry season on flood tides in the upper estuary, whereas ebb tide densities of these species prevailed in other regions. Environmental fluctuations associated with lunar periodicity, such as tidal amplitude, may account for weekly variability of recruitment and reproduction of some fish species. A. clupeoides showed increased spawning activity during first quarter moon, whereas new moon phases seemed to be reproduction periods of Cynoscion acoupa. Vertical migration was not employed by the most abundant species to enable river retention, since larval densities of these species were not significantly higher at the bottom on ebb tides, except for C. acoupa and Stellifer rastrifer. This result may be related to system turbulence or to the dominance of younger stages unable to migrate vertically at the time of sampling. Lateral movement to the river bank is proposed as a possible retention mechanism. Diel effects on larval abundance related to trophic activity and gear avoidance.