Major migration barriers have been identified as an important factor in the drastic reduction of freshwater eel stocks at the catchment scale. In this study, we developed a way to assist decision making in the management of migration barriers so as to increase eel presence throughout the Loire catchment (France). Models were developed according to eel size-class and various different management strategies to improve accessibility, taking into account: (i) all the migration barriers from the tidal limit to different upstream limits (downstream-upstream strategy), (ii) all the migration barriers with a given degree of passability (migration barrier passability class strategy), (iii) all the migration barriers in a given sub-catchment area (sub-catchment strategy) and (iv) all the migration barriers in the entire Loire catchment (global strategy). Eel were actually found to occur in the Loire at about 50% of the sites sampled. The improvement of habitat accessibility by removing all obstacles to colonisation or installing fish passes, for example (global strategy), would lead to eels being found throughout the whole river. If this management strategy is impossible because the high cost, two others, also producing significant eel continental colonisation must be implemented. Either all barriers from the tidal limit with medium passability and/or migration barriers in the sub-catchment area which is closest to the sea and least accessible must be managed. In both cases, the area significantly exploited by eels and the probability that this species will be present will be doubled. However, these results can only be counted on if the fluvial recruitment increases significantly.