The colonisation of Gironde (SW France) river catchment by three catadromous species juveniles, eel, Anguilla anguilla, flounder Platychtys flesus and thinlipp mullet Liza ramada was investigated comparatively using Sr/Ca and Ba/Ca composition of otolith. The relation between Sr/Ca and Ba/Ca in the otoliths and trace element concentration in water was validated with an experimental setting while the relation between Sr/Ca and Ba/Ca and habitat was validated with a 6 months caging experiment at four sites along the estuary-river gradient. 50 mullets, 30 eels and 47 flounders were collected in the Gironde river catchment. Otoliths were analysed with Femtosecond LA ICPMS along a trajectory from the core to the edge. A 20 micron wide laser beam was used together with a small ablation cell, providing high spatial resolution. Positions of annual checks were recorded to obtain time series. The validation demonstrated that all species incorporated Sr and Ba in their otoliths in proportion with water concentration. Based on Sr and Ba concentrations in the eel otoliths, the four caging sites of the catchment could be discriminated. A signal processing method based on Gaussian hidden Markov models was applied to the multi-elemental life histories data. The strength of this approach relied in its ability to provide a quantitative, automated analysis and classification of habitat use patterns without any a priori. Using Sr and Ba in synergy, allowed a finer geographic scale than using one alone. Together with the validation results, the analysis revealed that the three species used at least three different habitats during their growth phase along the catchment gradient. The three species had a large diversity of habitat use patterns with resident and nomadic tactics. The resident tactic was less frequent than the tactics using two or more habitats within each individual pattern. Mullet used more habitats in the lower part of the estuary than eel and flounders and changed habitats much more frequently. Eels and flounders tended to colonise first freshwater, and then estuarine habitats later in life while mullets used all the range of catchment habitats throughout their life.