We analysed length structure of European eel (Anguilla anguilla) stocks with a simple size-structured model including a linear trend of recruitment, a linear growth curve, a negative exponential mortality and a silvering process based on a gamma function. Eels shorter than 30 cm were excluded from the analysis in order to limit effect of sex determinism, colonization process and gear selectivity. The data sets used in this study were obtained from Water Framework Directive (WFD) survey and sampling that can be assimilated to Data Collection Regulation (DCR) survey in the Garonne and Dordogne basin covering seven WFD water bodies (from downstream estuary to upstream tributaries). Even if the calibration remained very sensitive to parameter boundaries, this approach allowed calculation of percentages of silver eels per settled yellow eels in each water bodies. The resulting percentages obtained for each water body matched our knowledge of the corresponding anthropogenic pressure levels. The information about eel stock status provided by the present analysis urges to implement management actions in freshwater estuary compartment. This analysis also showed that the trend in mean length of silver eels between compartments can be inversed only by changing mortality and growth. This result explained why longest eels are presently produced upstream where mortality rate is the lowest even though in putative pristine conditions, they would be produced in the estuary.