The aim of this study was to evaluate the impact of dredging activity to deepen the Port of Aratu on fish larvae assemblage structure. Samples were collected before, during and after dredging and at 6 sampling stations during both the flod and ebb tide (only during the dry season). Ichthyoplankton was collected through surface hauls using a bongo net with a 500μm mesh size. Oceanographic variables (temperature and salinity), water quality (dissolved oxygen and turbidity) and nutrients (ammonia and total phosphorus) were obtained simultaneously. During dredging, the lowest density of eggs and larvae, family richness and diversity were registered, with a subsequent recovery observed after dredging. Multivariate ordination showed the great differences between samplings, which demonstrated temporal variability in the distribution and abundance of ichthyoplankton in the port of Aratu (Bahia, Northeastern Brazil), in response to the seasonality of oceanographic characteristics of the water masses and changes in water quality, possibly associated with dredging activities.