The development of the Water Framework Directive aimed to establish an integrated framework of water management at European level. This framework revolves around inland surface waters, transitional waters, coastal waters and ground waters. In the process of achieving the environment and ecological objectives set from the Directive, the role of economics is put in the core of the water management. An important feature of the Directive is the recovery of total economic cost of water services by all users. The total cost of water services can be disaggregated into environmental, financial and resource costs. Another important aspect of the directive is the identification of major drivers and pressures in each River Basin District. We describe a methodology that is aiming to achieve sustainable and environmental and socioeconomic management of freshwater ecosystem services. The Ecosystem Services Approach is in the core of the suggested methodology for the implementation of a more sustainable and efficient water management. This approach consists of the following three steps: (i) socio-economic characterization of the River Basin area, (ii) assessment of the current recovery of water use cost, and (iii) identification and suggestion of appropriate programs of measures for sustainable water management over space and time. This methodology is consistent with a) the economic principles adopted explicitly by the Water Framework Directive (WFD), b) the three-step WFD implementation approach adopted in the WATECO document, c) the Ecosystem Services Approach to valuing freshwater goods and services to humans. Furthermore, we analyze how the effects of multiple stressors and socio-economic development can be quantified in the context of freshwater resources management. We also attempt to estimate the value of four ecosystem services using the benefit transfer approach for the Anglian River Basin, which showed the significance of such services.