Stocks of European eel (Anguilla anguilla) have declined continuously and steadily, since 1980. A model, GEMAC, namely Glass Eel Model to Assess Compliance, has been developed with the objective of assessing anthropogenic impacts on glass eels in estuaries and evaluating the effects of management measures, to support initiatives aimed at helping the eel stocks recover. The model is described and applied to two estuaries with contrasting anthropogenic pressures: the Vilaine and the Garonne. It assesses the proportion of settled glass eels relative to a non-impacted situation with current (%S/R) or pristine recruitment (%S/R0). The estimated %S/R (%S/R0) is 5.5% (1.1%) for the Vilaine and 78% (19%) for the Garonne, in accord with the different levels of anthropogenic pressure in these two estuaries. A sensitivity analysis shows that the assessment of %S/R is accurate, and that in a data-poor context, the %S/R is under-assessed, as required by the precautionary approach. Seven management scenarios are explored all aiming to halve the anthropogenic pressure, but in fact leading to different levels of glass eel escapement, from almost zero to a 13-fold increase. This variation emphasizes the need for the estuarine context of eel stock management to be carefully evaluated for effectiveness when implementing management measures.