We explored the capacity of the biological and hydromorphological indices used in the Water Framework Directive (WFD) to assess ecosystem services by evaluating the ecological status of Spanish River Basins. This analysis relies on an exhaustive bibliography review which showed scientific evidence of the interlinkages between some ecosystem services and different hydromorphological and biological elements which have been used as indices in the WFD. Our findings indicate that, of a total of 38 ecosystem services analyzed, biological and hydromorphological indices can fully evaluate four ecosystem services. In addition, 18 ecosystem services can be partly evaluated by some of the analyzed indices, while 11 are not related with the indices. While Riparian Forest Quality was the index that was able to assess the largest number of ecosystem services (N = 12), the two indices of macrophytes offered very poor guarantees. Finally, biological indices related to diatoms and aquatic invertebrates and the Fluvial Habitat Index can be related with 7, 6, and 6 ecosystem services, respectively. Because the WFD indices currently used in Spain are not able to assess most of the ecosystem services analyzed, we suggest that there is potential to develop the second phase of the WFD implementation taking this approach into consideration. The incorporation of the ecosystem services approach into the WFD could provide the framework for assess the impacts of human activities on the quality of fluvial ecosystems and could give insights for water and watershed management in order to guarantee the delivery of multiple ecosystem services.