An individual-based model (IBM) based on SimAqualife framework was used to investigate the effects of physical and biological variables on the transport via tidal currents of glass eel (Anguilla anguilla) through the Gironde estuary. This approach could be useful to understand further the glass eel behaviour and to explain the river recruitment variability in this economically and ecologically important species. By coupling a particle-tracking model integrating fish behaviour with the 2D hydrodynamic model SiAM we could assess the influences of spatial and temporal location of departure and various synchronisation modes for vertical migration on transport success and transport paths. Results from the model indicate that the synchronisation mode is the major determinant on transport success and that departure location effect the final destination between the two main tributaries of the Gironde estuary. The comparison between model outputs and patterns observed in scientific survey highlights the necessity to precise the mechanisms which lead glass-eel to abandon selective tidal transport. At least this IBM may be useful as a generic prototype for other animals using selective tidal stream transport .