Biodiversity recovery measures have often been ignored when dealing with the restoration of degraded aquatic systems. Furthermore, biological valuation methods have been applied only spatially in previous studies, and not jointly on a temporal and spatial scale. The intense monitoring efforts carried out in a highly polluted estuary, in northern Spain (Nervión estuary), allowed for the economic valuation of the costs and the biological valuation of the benefits associated with a 21 years sewage scheme application. The analysis show that the total amount of money invested into the sewage scheme has contributed to the estuary's improvement of both environmental and biological features, as well as to an increase in the uses and services provided by the estuary. However, the inner and outer parts of the estuary showed different responses. An understanding of the costs and trajectories of the environmental recovery of degraded aquatic systems is increasingly necessary to allow policy makers and regulators to formulate robust, cost-efficient and feasible management decisions.