The European eel (Anguilla anguilla) is drastically declining in all its distribution area and listed in the red list of the IUCN (International Union for Conservation of Nature). A rebuilding plan was adopted at European level in 2007, Regulation R(CE) 100/2007, to restore eel abundance to the level observed during the seventies. Its implementation started on the 1st of January 2009. This species is heavily threatened by numerous activities including fishing, and its management can only be effective through a systemic approach minimizing the whole range of human-induced impacts on the resource and its habitat. In the framework of the European interregional programme INTERREG IIIB-Atlantic Area– the INDICANG project aimed at elaborating abundance indicators of the European eel in the central part of its distribution area (http://www.ifremer/fr/indicang/). A methodological guide was elaborated by this project to define the indicators needed for this resource assessment. In this framework, Ifremer (Institut Français pour l'Exploitation de la Mer) and the UPPA University (Université de Pau et des Pays de l'Adour) have developed a method to estimate the daily and seasonal biomass of glass eels with the view to evaluate the fishery's impact on the estuarine eel recruitment to the Adour catchment. The estimation method uses observations from nightly scientific surveys to estimate glass eels' densities in the water column during various flood tides characterized by different hydrodynamic conditions. Information on these conditions allows the estimation of the glass eels biomass migrating during the night. From these estimates and reported catches made by the fishery during the same night, the exploitation rate applied by the fishery on the flow of glass eels progressing upstream during night flood tides is estimated. The relationship between the exploitation rate, fishery catches and hydrodynamic conditions allowed the estimation of the exploitation rate and nocturnal biomass fluctuations during the fishing season, from November 1st to March 31st of the following year. Finally, from the chronological series of biomass migrating at night, the total biomass migrating every day and the total recruitment into the estuary, during the main glass eel migration period, are estimated. Estimations made between 1998 and 2005 indicate that the overall rate of exploitation of the marine and continental fisheries, on average, is of 15.7%, ranging between 8 and 25% according to fishing seasons.