Resumen: The Georgescu-Roegen's statements about the connexion between the Economy and the Thermodynamics, together with the Eco-integrator approach introduced by Naredo after analyzing the water cost definitions given in the European Water Framework Directive (WFD), and the theory of the thermoeconomic cost proposed by Valero, are the outline backgrounds of the work presented in this study. Assuming that the physical laws are called to be the objective and universal tools to assess water costs, Physical Hydronomics (PH) has been developed as the accounting tool for the WFD application. PH is defined as the specific application of the Thermodynamics to physically characterize the degradation and correction of water bodies. The Second Law of Thermodynamics, through the exergy loss calculation, is the basic working tool in this study. The final objective of PH is to use those calculated physical costs as a guide to allocate the environmental and resource costs proposed by the WFD by 2015. In this dissertation, the general framework, the foundations, and the accounting principles of PH are developed. Firstly, WFD was carefully studied an interpreted from a Thermodynamics perspective. The different water costs defined in the Directive were translated into exergy concepts and the study hypothesis was established. The diverse river statuses proposed by the Directive were defined in exergy terms by means of their quantity and quality characterization. Secondly, from the quantity and quality measurements in the river (they give the exergy value to water bodies), the exergy profiles of the river at different statuses (those defined by the WFD) are obtained. Then, the environmental cost of water is obtained (in energy units) as the exergy needed to cover the gap between the current state of the river and the objective state defined by the applicable legislation to fulfil the European requirements. To do it, the thermodynamic efficiency of water treatment technologies was introduced in the analysis. In the last step, the water costs, calculated in energy units, are converted in economic units by introducing the energy price. Moreover, Physical Hydronomics presents an important advantage in relation to other approaches: costs can be allocated according to the degradation (exergy costs) provoked by the different water users in the water bodies. The Polluter Pays Principle stated by the WFD can be therefore implemented. In addition to that, PH overcomes the proposal by defining the Degrader Pays Principle, which joins the quantitative and qualitative water degradation of water within the analysis. To illustrate the application of the PH methodology, two case studies were developed: the Muga and the Foix watersheds, both located in the Inland Basins of Catalonia, but with quite different characteristics features. The results show that similar results to conventional Measurements Plans to fulfil the WFD objectives are obtained. However, the cost allocation can be performed within this methodology attending to an objective measurement, the water degradation due to each water use. The last part of this dissertation is devoted to a methodology different from the PH: the emergy approach. The WFD costs are defined according to the emergy basis and the hypothetical real price of water is obtained. In this case, there is not any projection to 2015, just an evaluation of the current situation of the Foix watershed, which is the river basin selected to show the methodology.