As marine protected areas (MPAs) are increasingly being utilised as a tool for fisherymanagement, their impact on the food web needs to be fully understood. However, little isknown about the effect of MPAs on fish assemblages, especially in the presence ofdifferent life history and ecological traits. Modelling the observed changes in fishpopulation structures may provide a mechanistic understanding of fish assemblage dynamics.In addition, modelling allows a quantitative estimate of MPA spill-over. To achieve thispurpose, we adapted an existing ecosystem model, OSMOSE (Object-oriented simulator ofmarine biodiversity exploitation), to the specific case of the presence of fish withmultiple life histories. The adapted model can manage 4 main categories of life historyidentified in an estuary MPA: fish that (1) spend their entire life cycle locally, (2) arepresent only as juveniles, (3) enter the area as juveniles and stay permanently exceptduring reproduction periods, which occur outside the estuary, and (4) are presentoccasionally and for a short time for foraging purposes. To take into account thesespecific life-history traits, the OSMOSE code was modified. This modelling approach wasdeveloped in the context of the Bamboung Bolong MPA, located in a mangrove area in theSine-Saloum Delta, Senegal. This was the ideal case to develop our approach as there hasbeen scientific monitoring of the fish population structure inside the MPA before fisheryclosure, providing a reference state, and continuous monitoring since the closure.Ecologically similar species were pooled by trophic traits into 15 groups that represented97% of the total biomass. Lower trophic levels (LTL) were represented by 6 compartments.The biomass of the model species was calibrated to reproduce the reference situationbefore fishery closure. Model predictions of fish assemblage changes after fishery closurecorresponding to the Bamboung MPA creation scenario were compared to field observations;in most cases the model reproduces observed changes in biomass (at least in direction). Wesuggest the existence of a “sanctuary effect”, that was not taken into account in themodel, this could explain the observed increase in biomass of top predators not reproducedby the model. Finally, the annual MPA fish spill-over was estimated at 11 tons (~33% ofthe fish biomass) from the model output, mainly due to diffusive effects.