The influence of oceanic circulation and bathymetry on the fish larvae retention inside Mejillones Bay, northern Chile, was examined. Fish larvae were collected during two coastal upwelling events in November 1999 and January 2000. An elevated fish larvae accumulation was found near an oceanic front and a zone of low-speed currents. Three groups of fish larvae were identified: the coastal species (Engraulis ringens and Sardinops sagax), associated with high chlorophyll-a levels; larvae from the families Phosichthyidae (Vinciguerria lucetia) and Myctophidae (Diogenichthys laternatus and Triphoturus oculeus), associated with the thermocline (12°C), and finally, larvae of the families Myctophidae (Diogenichthys atlanticus) and Bathylagidae (Bathylagus nigrigenys), associated with high values of temperature and salinity. The presence of a seamount and submarine canyon inside Mejillones Bay appears to play an important role in the circulation during seasonal upwelling events. We propose a conceptual model of circulation and particles retention into Mejillones Bay. The assumption is that during strong upwelling conditions the flows that move along the canyon emerge in the centre of Mejillones Bay, producing a fish larvae retention zone. Understanding the biophysical interactions responsible to trap and/or concentrate particles is essential to protect these fragile upwelling ecosystems.