The aim of this work was to develop a methodological framework for the management of local eel stocks that integrates habitat restoration with optimal fishery management. The Bolsena lake (Viterbo, Italy) and its emissary, the river Marta, were taken as a reference system. The river flows in the Mediterranean sea but its course is fragmented by a number of dams built in the past century preventing eel migration from and to the sea. Eel fishery in the Bolsena lake is thus sustained by periodic stocking of glass eels caught at the Marta river estuary. A detailed demographic model was applied to simulate fishery yields and potential spawner escapement under different recruitment and management scenarios. It was estimated that the high exploitation rates occurring in the nineties reduced the potential spawner escapement from the Bolsena lake to less than 1 t; under current harvesting rates, the potential spawner escapement is estimated in about 12 t while in pristine conditions (i.e. high recruitment and no fishing) estimated spawner escapement is about 21 t. This analysis thus showed that current fishery management would comply with the 40% spawner escapement requirement of the EU regulation 1100/2007 if the connections between the Bolsena lake emissary and the sea were fully re-established. This confirms the opportunity of an integrated approach to management at the catchment area level scale for eel populations, that shall hopefully contribute to the conservation of the global stock.